def _saveRemark(self, structure, filePDB): #Structure Errors standard = FcfrpStandardizationPDBErrorDetails() for k,v in structure.get_StructureErrors().getStructureErrors().iteritems(): m = standard.formatMessageError(v.getIdError(), v.getMessage()) values = ( self._REMARK, m ) filePDB.write(self._REMARK_FORMAT % values)
def setStructureErrors(self,errors,vs, standard = None): if standard == None: standard = FcfrpStandardizationPDBErrorDetails() dic = {} for e in errors: if e == 1: dic = standard.standardization(e,vs.getMissingResidues()) self._setError(dic, e) elif e == 2: dic = standard.standardization(e,vs.getMissingAtoms()) self._setError(dic, e) elif e == 3: dic = standard.standardization(e,vs.getDuplicatedAtoms()) self._setError(dic, e) elif e == 4: dic = standard.standardization(e,vs.getUnknownResidues()) self._setError(dic, e)