How to use the moltemplate.genpoly_lt.WrapPeriodic.Wrap function in moltemplate

def ChooseDirections(self, coords):
        """
        Calculate the direction each monomer subunit should be pointing at:

        """

        N = len(coords)
        self.direction_vects = [[0.0, 0.0, 0.0] for i in range(0, N + 1)]

        if self.settings.is_circular:
            for i in range(0, N):
                # By default, the direction that monomer "i" is pointing is
                # determined by the position of the monomers before and after it
                # (at index i-1, and i+1).  More generally, we allow the user
                # to choose what these offsets are ("dir_index_offsets[")
                ia = WrapPeriodic.Wrap(i + self.settings.dir_index_offsets[0],
                                       N)
                ib = WrapPeriodic.Wrap(i + self.settings.dir_index_offsets[1],
                                       N)
                for d in range(0, 3):
                    self.direction_vects[i][d] = coords[ib][d] - coords[ia][d]
                        
        else:
            for i in range(1, N - 1):
                for d in range(0, 3):
                    self.direction_vects[i][d] = coords[
                        i + self.settings.dir_index_offsets[1]][d] - coords[
                            i + self.settings.dir_index_offsets[0]][d]

            for d in range(0, 3):
                self.direction_vects[0][d] = coords[1][d] - coords[0][d]
                self.direction_vects[N-1][d] = coords[N-1][d] - coords[N-2][d]

assert(len(self.settings.bonds_name) ==
               len(self.settings.bonds_type) ==
               len(self.settings.bonds_atoms) ==
               len(self.settings.bonds_index_offsets))
        if len(self.settings.bonds_type) > 0:
            outfile.write("\n"
                          "\n"
                          "write(\"Data Bonds\") {\n")
        WrapPeriodic.bounds_err = False
        for i in range(0, N):
            test = False
            for b in range(0, len(self.settings.bonds_type)):
                I = i + self.settings.bonds_index_offsets[b][0]
                J = i + self.settings.bonds_index_offsets[b][1]
                I = WrapPeriodic.Wrap(I, N)
                J = WrapPeriodic.Wrap(J, N)
                if WrapPeriodic.bounds_err:
                    WrapPeriodic.bounds_err = False
                    if not self.settings.connect_ends:
                        continue
                outfile.write(
                    "  $bond:" + self.settings.bonds_name[b] + str(i + 1))
                if len(self.settings.bonds_type) > 1:
                    outfile.write("_" + str(b + 1))
                outfile.write(" @bond:" + self.settings.bonds_type[b] + " $atom:mon[" + str(I) + "]/" + self.settings.bonds_atoms[
                              b][0] + " $atom:mon[" + str(J) + "]/" + self.settings.bonds_atoms[b][1] + "\n")
        if len(self.settings.bonds_type) > 0:
            outfile.write("}  # write(\"Data Bonds\") {...\n\n\n")

        assert(len(self.settings.angles_name) ==
               len(self.settings.angles_type) ==

len(self.settings.impropers_type) ==
               len(self.settings.impropers_atoms) ==
               len(self.settings.impropers_index_offsets))
        if len(self.settings.impropers_type) > 0:
            outfile.write("\n"
                          "\n"
                          "write(\"Data Impropers\") {\n")
        for i in range(0, N):
            for b in range(0, len(self.settings.impropers_type)):
                I = i + self.settings.impropers_index_offsets[b][0]
                J = i + self.settings.impropers_index_offsets[b][1]
                K = i + self.settings.impropers_index_offsets[b][2]
                L = i + self.settings.impropers_index_offsets[b][3]
                I = WrapPeriodic.Wrap(I, N)
                J = WrapPeriodic.Wrap(J, N)
                K = WrapPeriodic.Wrap(K, N)
                L = WrapPeriodic.Wrap(L, N)
                if WrapPeriodic.bounds_err:
                    WrapPeriodic.bounds_err = False
                    if not self.settings.connect_ends:
                        continue
                outfile.write("  $improper:" +
                              self.settings.impropers_name[b] + str(i + 1))
                if len(self.settings.impropers_type) > 1:
                    outfile.write("_" + str(b + 1))
                outfile.write(" @improper:" + self.settings.impropers_type[b] +
                              " $atom:mon[" + str(I) + "]/" + self.settings.impropers_atoms[b][0] +
                              " $atom:mon[" + str(J) + "]/" + self.settings.impropers_atoms[b][1] +
                              " $atom:mon[" + str(K) + "]/" + self.settings.impropers_atoms[b][2] +
                              " $atom:mon[" + str(L) + "]/" + self.settings.impropers_atoms[b][3] +
                              "\n")
        if len(self.settings.impropers_type) > 0:

assert(len(self.settings.dihedrals_name) ==
               len(self.settings.dihedrals_type) ==
               len(self.settings.dihedrals_atoms) ==
               len(self.settings.dihedrals_index_offsets))
        if len(self.settings.dihedrals_type) > 0:
            outfile.write("\n"
                          "\n"
                          "write(\"Data Dihedrals\") {\n")
        for i in range(0, N):
            for b in range(0, len(self.settings.dihedrals_type)):
                I = i + self.settings.dihedrals_index_offsets[b][0]
                J = i + self.settings.dihedrals_index_offsets[b][1]
                K = i + self.settings.dihedrals_index_offsets[b][2]
                L = i + self.settings.dihedrals_index_offsets[b][3]
                I = WrapPeriodic.Wrap(I, N)
                J = WrapPeriodic.Wrap(J, N)
                K = WrapPeriodic.Wrap(K, N)
                L = WrapPeriodic.Wrap(L, N)
                if WrapPeriodic.bounds_err:
                    WrapPeriodic.bounds_err = False
                    if not self.settings.connect_ends:
                        continue
                outfile.write("  $dihedral:" +
                              self.settings.dihedrals_name[b] + str(i + 1))
                if len(self.settings.dihedrals_type) > 1:
                    outfile.write("_" + str(b + 1))
                outfile.write(" @dihedral:" + self.settings.dihedrals_type[b] +
                              " $atom:mon[" + str(I) + "]/" + self.settings.dihedrals_atoms[b][0] +
                              " $atom:mon[" + str(J) + "]/" + self.settings.dihedrals_atoms[b][1] +
                              " $atom:mon[" + str(K) + "]/" + self.settings.dihedrals_atoms[b][2] +
                              " $atom:mon[" + str(L) + "]/" + self.settings.dihedrals_atoms[b][3] +
                              "\n")

len(self.settings.dihedrals_atoms) ==
               len(self.settings.dihedrals_index_offsets))
        if len(self.settings.dihedrals_type) > 0:
            outfile.write("\n"
                          "\n"
                          "write(\"Data Dihedrals\") {\n")
        for i in range(0, N):
            for b in range(0, len(self.settings.dihedrals_type)):
                I = i + self.settings.dihedrals_index_offsets[b][0]
                J = i + self.settings.dihedrals_index_offsets[b][1]
                K = i + self.settings.dihedrals_index_offsets[b][2]
                L = i + self.settings.dihedrals_index_offsets[b][3]
                I = WrapPeriodic.Wrap(I, N)
                J = WrapPeriodic.Wrap(J, N)
                K = WrapPeriodic.Wrap(K, N)
                L = WrapPeriodic.Wrap(L, N)
                if WrapPeriodic.bounds_err:
                    WrapPeriodic.bounds_err = False
                    if not self.settings.connect_ends:
                        continue
                outfile.write("  $dihedral:" +
                              self.settings.dihedrals_name[b] + str(i + 1))
                if len(self.settings.dihedrals_type) > 1:
                    outfile.write("_" + str(b + 1))
                outfile.write(" @dihedral:" + self.settings.dihedrals_type[b] +
                              " $atom:mon[" + str(I) + "]/" + self.settings.dihedrals_atoms[b][0] +
                              " $atom:mon[" + str(J) + "]/" + self.settings.dihedrals_atoms[b][1] +
                              " $atom:mon[" + str(K) + "]/" + self.settings.dihedrals_atoms[b][2] +
                              " $atom:mon[" + str(L) + "]/" + self.settings.dihedrals_atoms[b][3] +
                              "\n")
        if len(self.settings.dihedrals_type) > 0:
            outfile.write("}  # write(\"Data Dihedrals\") {...\n\n\n")

Calculate the direction each monomer subunit should be pointing at:

        """

        N = len(coords)
        self.direction_vects = [[0.0, 0.0, 0.0] for i in range(0, N + 1)]

        if self.settings.is_circular:
            for i in range(0, N):
                # By default, the direction that monomer "i" is pointing is
                # determined by the position of the monomers before and after it
                # (at index i-1, and i+1).  More generally, we allow the user
                # to choose what these offsets are ("dir_index_offsets[")
                ia = WrapPeriodic.Wrap(i + self.settings.dir_index_offsets[0],
                                       N)
                ib = WrapPeriodic.Wrap(i + self.settings.dir_index_offsets[1],
                                       N)
                for d in range(0, 3):
                    self.direction_vects[i][d] = coords[ib][d] - coords[ia][d]
                        
        else:
            for i in range(1, N - 1):
                for d in range(0, 3):
                    self.direction_vects[i][d] = coords[
                        i + self.settings.dir_index_offsets[1]][d] - coords[
                            i + self.settings.dir_index_offsets[0]][d]

            for d in range(0, 3):
                self.direction_vects[0][d] = coords[1][d] - coords[0][d]
                self.direction_vects[N-1][d] = coords[N-1][d] - coords[N-2][d]

        # Optional: normalize the direction vectors

assert(len(self.settings.dihedrals_name) ==
               len(self.settings.dihedrals_type) ==
               len(self.settings.dihedrals_atoms) ==
               len(self.settings.dihedrals_index_offsets))
        if len(self.settings.dihedrals_type) > 0:
            outfile.write("\n"
                          "\n"
                          "write(\"Data Dihedrals\") {\n")
        for i in range(0, N):
            for b in range(0, len(self.settings.dihedrals_type)):
                I = i + self.settings.dihedrals_index_offsets[b][0]
                J = i + self.settings.dihedrals_index_offsets[b][1]
                K = i + self.settings.dihedrals_index_offsets[b][2]
                L = i + self.settings.dihedrals_index_offsets[b][3]
                I = WrapPeriodic.Wrap(I, N)
                J = WrapPeriodic.Wrap(J, N)
                K = WrapPeriodic.Wrap(K, N)
                L = WrapPeriodic.Wrap(L, N)
                if WrapPeriodic.bounds_err:
                    WrapPeriodic.bounds_err = False
                    if not self.settings.connect_ends:
                        continue
                outfile.write("  $dihedral:" +
                              self.settings.dihedrals_name[b] + str(i + 1))
                if len(self.settings.dihedrals_type) > 1:
                    outfile.write("_" + str(b + 1))
                outfile.write(" @dihedral:" + self.settings.dihedrals_type[b] +
                              " $atom:mon[" + str(I) + "]/" + self.settings.dihedrals_atoms[b][0] +
                              " $atom:mon[" + str(J) + "]/" + self.settings.dihedrals_atoms[b][1] +
                              " $atom:mon[" + str(K) + "]/" + self.settings.dihedrals_atoms[b][2] +
                              " $atom:mon[" + str(L) + "]/" + self.settings.dihedrals_atoms[b][3] +