How to use the pyscal.catom function in pyscal

headerdict["x"] = headerdict.pop("xs")
                    headerdict["y"] = headerdict.pop("ys")
                    headerdict["z"] = headerdict.pop("zs")
                else:
                    raise ValueError("only x/xs, y/ys andz/zs keys are allowed for traj file")


        else:
            raw = line.strip().split()
            idd = int(raw[headerdict["id"]])
            typ = int(raw[headerdict["type"]])
            x = float(raw[headerdict["x"]])
            y = float(raw[headerdict["y"]])
            z = float(raw[headerdict["z"]])

            atom = pca.Atom()
            atom.pos = [x, y, z]
            atom.id = idd
            atom.type = typ
            atom.loc = count-8

            customdict = {}
            #if customkeys need to be read, do it
            if customread:
                for cc, kk in enumerate(customkeys):
                    customdict[kk] = raw[headerdict[kk]]

            atom.custom = customdict
            atoms.append(atom)

    #close files
    f.close()

if (x < xlow):
                x = x + (xhigh - xlow)
            elif (x > xhigh):
                x = x - (xhigh - xlow)
            if (y < ylow):
                y = y + (yhigh - ylow)
            elif (y > yhigh):
                y = y - (yhigh - ylow)
            if (z < zlow):
                z = z + (zhigh - zlow)
            elif (z > zhigh):
                z = z - (zhigh - zlow)

            count+=1
            idd = count
            atom = pca.Atom()
            atom.pos = [x, y, z]
            atom.id = idd
            atom.type = typ
            atom.loc = i-atom_start
            #atom = pc.Atom(pos=, id=idd, type=typ)
            atoms.append(atom)
            i+=1
        else:
            species+=1

    return atoms, boxdims

atoms = []
    xh = nx*lattice_constant*xfact
    yh = ny*lattice_constant*yfact
    zh = nz*lattice_constant*zfact
    boxdims = [[0, xh], [0, yh], [0, zh]]

    #create structure
    for i in range(1, nx+1):
        for j in range(1, ny+1):
            for k in range(1, nz+1):
                for l in range(1, coord_no+1):
                    m += 1
                    posx = (unitcellx[l-1]+(lattice_constant*xfact*(float(i)-1)))
                    posy = (unitcelly[l-1]+(lattice_constant*yfact*(float(j)-1)))
                    posz = (unitcellz[l-1]+(lattice_constant*zfact*(float(k)-1)))
                    atom = pc.Atom()
                    atom.pos = [posx, posy, posz]
                    atom.id = co
                    atom.type = atomtype[l-1]
                    atom.loc = co-1
                    atoms.append(atom)
                    co += 1

    return atoms, boxdims