def init_residue()

in data/xpdb.py [0:0]

• 25 lines of code
• 12 McCabe index (conditional complexity)

    def init_residue(self, resname, field, resseq, icode):
        """Initiate a new Residue object.

        Arguments:
            resname: string, e.g. "ASN"
            field: hetero flag, "W" for waters, "H" for hetero residues, otherwise blanc.
            resseq: int, sequence identifier
            icode: string, insertion code

        Return:
            None
        """
        if field != " ":
            if field == "H":
                # The hetero field consists of
                # H_ + the residue name (e.g. H_FUC)
                field = "H_" + resname
        res_id = (field, resseq, icode)

        if resseq > self.max_resseq:
            self.max_resseq = resseq

        if field == " ":
            fudged_resseq = False
            while self.chain.has_id(res_id) or resseq == 0:
                # There already is a residue with the id (field, resseq, icode)
                # resseq == 0 catches already wrapped residue numbers which
                # do not trigger the has_id() test.
                #
                # Be sloppy and just increment...
                # (This code will not leave gaps in resids... I think)
                #
                # XXX: shouldn't we also do this for hetero atoms and water??
                self.max_resseq += 1
                resseq = self.max_resseq
                res_id = (field, resseq, icode)  # use max_resseq!
                fudged_resseq = True

            if fudged_resseq and self.verbose:
                sys.stderr.write(
                    "Residues are wrapping (Residue "
                    + "('%s', %i, '%s') at line %i)."
                    % (field, resseq, icode, self.line_counter)
                    + ".... assigning new resid %d.\n" % self.max_resseq
                )
        residue = Residue(res_id, resname, self.segid)
        self.chain.add(residue)
        self.residue = residue
        return None