def run(args, log=sys.stdout):
pdb_h = iotbx.pdb.input(source_info=None, file_name=args[0]).\
construct_hierarchy()
r = ramachandran_eval.RamachandranEval()
outp = list_rama_outliers_h(pdb_h, r.rama_eval)
print(outp)
print("END")
def _score_conformation(self, O_atom, C_atom, N_atom, chain_around, angle):
# gs = self.model.geometry_statistics()
# gs.show()
# print "MOLPROBITY Score:", gs.result().molprobity_score
# print "Cablam outliers:", gs.result().cablam.outliers
# print "Clashscore: ", gs.result().clash.score
hbonds = self._search_hbond(O_atom, C_atom, N_atom, chain_around)
ro = list_rama_outliers_h(chain_around.get_hierarchy())
cab_results = cablamalyze(
pdb_hierarchy=chain_around.get_hierarchy(),
outliers_only=True,
out=null_out(),
quiet=True,
cablam_contours = self.cablam_contours,
ca_contours = self.ca_contours,
motif_contours = self.motif_contours,
)
outliers_only = [x for x in cab_results.results if x.feedback.cablam_outlier]
return (angle, len(ro.split("\n"))-1, len(outliers_only), hbonds)
