diff --git a/pyproject.toml b/pyproject.toml
index b63a1725..e535eee4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -93,4 +93,9 @@ replace = 'version = "{new_version}"'
 [[tool.bumpversion.files]]
 filename = "src/poli/__init__.py"
 search = '__version__ = "{current_version}"'
-replace = '__version__ = "{new_version}"'
\ No newline at end of file
+replace = '__version__ = "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "setup.cfg"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
index 55c8c5ed..253dc225 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = poli
-version = "1.0.0.dev0"
+version = "1.0.0.dev2"
 author_email = miguel.gonzalez-duque@bio.ku.dk
 description = Protein Objectives Library
 long_description = file: README.md
diff --git a/src/poli/core/util/chemistry/smiles_alphabet.py b/src/poli/core/util/chemistry/smiles_alphabet.py
new file mode 100644
index 00000000..ddff9e1c
--- /dev/null
+++ b/src/poli/core/util/chemistry/smiles_alphabet.py
@@ -0,0 +1,2349 @@
+CID_SMILES_COUNTS = {
+    "": 44420414080,
+    "C": 2501779041,
+    "=": 923142831,
+    "(": 660472511,
+    ")": 660472511,
+    "O": 350079998,
+    "N": 325800358,
+    "1": 256135776,
+    "2": 208175970,
+    "3": 137611186,
+    "4": 78117092,
+    "F": 53547041,
+    "S": 44262279,
+    "5": 37744044,
+    "[C@H]": 29592982,
+    "[C@@H]": 29562650,
+    "Cl": 27583359,
+    "/": 27499221,
+    ".": 26383866,
+    "6": 19040680,
+    "7": 11946940,
+    "\\": 10219927,
+    "Br": 9309871,
+    "8": 8971834,
+    "[N+]": 7559684,
+    "9": 7089046,
+    "[O-]": 7077949,
+    "[C@@]": 3671846,
+    "[C@]": 3281384,
+    "[2H]": 3152821,
+    "P": 3123822,
+    "I": 2807425,
+    "[Si]": 2335956,
+    "[C-]": 1553009,
+    "B": 989657,
+    "[NH+]": 678291,
+    "[N-]": 666314,
+    "[Na+]": 451479,
+    "[B]": 410832,
+    "[HH]": 404315,
+    "[Cl-]": 363185,
+    "[Y]": 279710,
+    "[CH-]": 254408,
+    "[P+]": 214734,
+    "[Ir]": 206755,
+    "[NH2+]": 197772,
+    "[CH]": 197689,
+    "[CH3-]": 169626,
+    "[CH2-]": 158704,
+    "[K+]": 155674,
+    "[S+]": 136431,
+    "[Br-]": 135664,
+    "[Se]": 123182,
+    "[I-]": 116496,
+    "[B-]": 110600,
+    "[NH3+]": 107587,
+    "[3H]": 103034,
+    "[S-]": 99616,
+    "[Li+]": 99273,
+    "[Pt]": 93992,
+    "[C]": 93594,
+    "[O+]": 91731,
+    "[Sn]": 91285,
+    "[Pt+2]": 88838,
+    "[W]": 86357,
+    "[SiH]": 77344,
+    "[NH-]": 72058,
+    "[V]": 71935,
+    "[OH-]": 71660,
+    "[PH+]": 61439,
+    "[H-]": 55447,
+    "[SiH2]": 55377,
+    "[S@]": 52361,
+    "[S@@]": 51342,
+    "[Na]": 49490,
+    "[Ge]": 46495,
+    "[O-2]": 45698,
+    "%10": 44860,
+    "[Mg+2]": 43788,
+    "[K]": 41663,
+    "[Al]": 40513,
+    "[SiH3]": 39129,
+    "[Zr+2]": 37152,
+    "[CH2]": 35935,
+    "[NH4+]": 35325,
+    "[Zn+2]": 34238,
+    "%11": 33370,
+    "[Fe]": 32730,
+    "[Pd]": 31923,
+    "[Fe+2]": 30052,
+    "[OH+]": 29120,
+    "%12": 28668,
+    "[F-]": 28111,
+    "[Cu+2]": 28110,
+    "[P@]": 28050,
+    "[Co]": 28009,
+    "[Ca+2]": 27718,
+    "[Ti]": 27663,
+    "[P@@]": 27320,
+    "[Ir+3]": 26574,
+    "[As]": 26180,
+    "[Pd+2]": 26042,
+    "[Zn]": 25837,
+    "[C+]": 25663,
+    "[Zr]": 24917,
+    "[P-]": 24617,
+    "[Rb]": 24595,
+    "[Cu]": 24259,
+    "[U]": 23906,
+    "[13C]": 22163,
+    "%13": 22084,
+    "[Ni]": 21920,
+    "[Ru]": 19831,
+    "[H+]": 19611,
+    "[Ni+2]": 19363,
+    "[Te]": 18845,
+    "[NH2-]": 18549,
+    "[CH+]": 18135,
+    "[Ac]": 17967,
+    "[OH3+]": 17045,
+    "[O]": 16785,
+    "%14": 16552,
+    "[Cr]": 16517,
+    "[I+]": 16410,
+    "[13CH2]": 15876,
+    "[18F]": 15627,
+    "[Zr+4]": 15416,
+    "[OH2+]": 15244,
+    "[Mo]": 15048,
+    "[2HH]": 14854,
+    "[Mn]": 14791,
+    "[Ti+4]": 14733,
+    "[Tb]": 14689,
+    "[13CH]": 14239,
+    "[Li]": 14180,
+    "%15": 13950,
+    "[Cu+]": 13930,
+    "[Rb+]": 13858,
+    "[Cs+]": 13650,
+    "[Rf]": 12826,
+    "%16": 12596,
+    "[Sb]": 12251,
+    "[Co+2]": 12210,
+    "[Ar]": 12144,
+    "[Ag+]": 11556,
+    "[Au+]": 11441,
+    "[W+2]": 11335,
+    "%17": 11326,
+    "[Rh]": 11324,
+    "[Ru+2]": 11121,
+    "[Hg]": 11008,
+    "[Re]": 10156,
+    "[Ba+2]": 10114,
+    "[Ti+2]": 9859,
+    "[Pb]": 9607,
+    "[Ag]": 9569,
+    "[SH+]": 9510,
+    "[Al+3]": 9481,
+    "[CH2+]": 8633,
+    "[N@+]": 8469,
+    "%18": 8130,
+    "[Pt+4]": 8096,
+    "[N@@+]": 8082,
+    "[Mn+2]": 8058,
+    "[Hf]": 7877,
+    "[H]": 7476,
+    "[13CH3]": 7452,
+    "[Au]": 7412,
+    "[Bi]": 7351,
+    "[Fe+3]": 7344,
+    "[Y+3]": 7204,
+    "[U+2]": 7195,
+    "[Sn+2]": 6888,
+    "[Ga]": 6612,
+    "%19": 6572,
+    "[In]": 6540,
+    "[3HH]": 6484,
+    "[SH2+]": 6332,
+    "[Hf+4]": 6303,
+    "[Os]": 6239,
+    "[Zn+]": 6227,
+    "[V+2]": 5854,
+    "[Ca]": 5822,
+    "[N]": 5747,
+    "[Mg]": 5700,
+    "[Co+3]": 5643,
+    "%20": 5590,
+    "[SH-]": 5483,
+    "[Ti+3]": 5392,
+    "[15N]": 5013,
+    "[Si-]": 4981,
+    "[Zr+3]": 4687,
+    "[Gd+3]": 4659,
+    "%21": 4504,
+    "[15NH]": 4478,
+    "[Tl]": 4388,
+    "[Ru+]": 4386,
+    "[AlH3]": 4331,
+    "[CH3+]": 4257,
+    "[Cr+3]": 4073,
+    "[Cd]": 4020,
+    "[14C]": 4002,
+    "[BH3-]": 3970,
+    "%22": 3952,
+    "[Ru+3]": 3833,
+    "[S-2]": 3711,
+    "%23": 3674,
+    "[Gd]": 3671,
+    "[Sr+2]": 3519,
+    "[Se-]": 3519,
+    "[Cd+2]": 3504,
+    "[AlH2]": 3476,
+    "%24": 3398,
+    "%25": 3332,
+    "[Pd+]": 3231,
+    "[PH3+]": 3215,
+    "[AlH]": 3154,
+    "[Rh+2]": 3115,
+    "[PH2+]": 3112,
+    "[Sn+]": 3085,
+    "%26": 3044,
+    "[Au+3]": 2955,
+    "[SeH]": 2924,
+    "[Mn+3]": 2888,
+    "[Nb]": 2735,
+    "[Sb-]": 2680,
+    "[Ta]": 2673,
+    "[Hg+]": 2671,
+    "[14CH]": 2660,
+    "[Pr]": 2632,
+    "[13C@@H]": 2616,
+    "[Be+2]": 2612,
+    "[2H-]": 2605,
+    "[BH-]": 2592,
+    "[BH2-]": 2546,
+    "[La]": 2503,
+    "[Eu]": 2478,
+    "[Ce]": 2475,
+    "[11CH3]": 2422,
+    "[13C@H]": 2406,
+    "[Ti+]": 2314,
+    "[Os+2]": 2290,
+    "[IH+]": 2284,
+    "[Ni+3]": 2262,
+    "[NH]": 2232,
+    "[ClH+]": 2175,
+    "[Pb+2]": 2172,
+    "[Al+]": 2135,
+    "[125I]": 2111,
+    "[15NH2]": 2071,
+    "[Mo+2]": 2053,
+    "[La+3]": 1977,
+    "[Ba]": 1952,
+    "[Al-]": 1949,
+    "[Ce+3]": 1948,
+    "[18O]": 1943,
+    "[Si@@]": 1937,
+    "[Pt+]": 1928,
+    "[Si@]": 1906,
+    "[Sm]": 1904,
+    "[Cr+2]": 1879,
+    "[Eu+3]": 1875,
+    "[Nd]": 1839,
+    "[Rh+3]": 1825,
+    "[Hf+2]": 1805,
+    "[123I]": 1744,
+    "[Bi+3]": 1724,
+    "[Se+]": 1722,
+    "[Nd+3]": 1716,
+    "[3H-]": 1664,
+    "[PH-]": 1639,
+    "[GeH]": 1616,
+    "[Sn+4]": 1581,
+    "[Sc]": 1577,
+    "[Fm]": 1549,
+    "[SnH]": 1535,
+    "[Mo+4]": 1519,
+    "[Fe+4]": 1492,
+    "[Yb]": 1487,
+    "[14CH2]": 1486,
+    "[Dy+3]": 1481,
+    "[As+]": 1421,
+    "[10B]": 1405,
+    "[Sb+3]": 1372,
+    "[GeH2]": 1324,
+    "[AsH]": 1289,
+    "[SiH4]": 1287,
+    "[Hg+2]": 1275,
+    "[V+4]": 1267,
+    "[Si+]": 1249,
+    "[In+3]": 1221,
+    "[Al+2]": 1220,
+    "[Os+]": 1207,
+    "[Ga+3]": 1196,
+    "[Lu]": 1161,
+    "[BH4-]": 1153,
+    "[Tb+3]": 1145,
+    "[Fe+]": 1118,
+    "[Sr]": 1107,
+    "[Sn+3]": 1100,
+    "[131I]": 1082,
+    "%27": 1066,
+    "[Yb+3]": 1033,
+    "[Sm+3]": 1019,
+    "[SiH-]": 1010,
+    "[Tc]": 1002,
+    "[Sc+3]": 979,
+    "[Ru+4]": 952,
+    "[99Tc]": 942,
+    "[Po]": 941,
+    "[11C]": 919,
+    "[14CH3]": 902,
+    "[Ru+6]": 884,
+    "[Cs]": 868,
+    "[Er]": 863,
+    "[SH3+]": 863,
+    "[Ir+2]": 861,
+    "[Tl+]": 852,
+    "[Dy]": 829,
+    "[GeH3]": 829,
+    "[99Tc+4]": 823,
+    "[Er+3]": 823,
+    "[Se-2]": 822,
+    "[PH4+]": 807,
+    "[Ho]": 802,
+    "[Si+4]": 778,
+    "[No]": 773,
+    "[Pr+3]": 760,
+    "[Th]": 758,
+    "[BiH2]": 741,
+    "[S]": 741,
+    "[Nb+5]": 728,
+    "[11B]": 727,
+    "%28": 726,
+    "[Si-2]": 718,
+    "[Ta+5]": 707,
+    "[Fe+6]": 689,
+    "[P]": 677,
+    "[Te+]": 674,
+    "[18OH]": 672,
+    "[SnH2]": 671,
+    "[Ce+4]": 664,
+    "[BH]": 662,
+    "[Fe+5]": 643,
+    "[As-]": 637,
+    "[1H]": 636,
+    "[Lu+3]": 626,
+    "[19F]": 622,
+    "[Os+4]": 618,
+    "[U+4]": 618,
+    "[IH2+]": 598,
+    "[Tm]": 586,
+    "[Cr+6]": 563,
+    "[Mo+3]": 548,
+    "%29": 532,
+    "[Th+4]": 526,
+    "[Ho+3]": 521,
+    "[PH2-]": 514,
+    "[124I]": 509,
+    "[At]": 506,
+    "[Cm]": 499,
+    "[SbH]": 493,
+    "[Co+]": 492,
+    "[GaH]": 487,
+    "[Bi+2]": 485,
+    "[SnH3]": 480,
+    "[AsH2]": 474,
+    "[15N+]": 471,
+    "[Cr+]": 470,
+    "[13C@@]": 461,
+    "[Cl+]": 458,
+    "[GaH3]": 457,
+    "[Be]": 453,
+    "[Np]": 448,
+    "[Eu+2]": 446,
+    "[Sg]": 444,
+    "[GeH4]": 440,
+    "[14C@@H]": 438,
+    "%30": 438,
+    "[Lr]": 431,
+    "[Tc+4]": 430,
+    "[13C@]": 412,
+    "[76Br]": 409,
+    "[Cr+4]": 409,
+    "[Xe]": 408,
+    "[ClH2+]": 407,
+    "%31": 406,
+    "[U+3]": 405,
+    "[10BH2]": 402,
+    "[TeH]": 401,
+    "[14C@H]": 400,
+    "[Ru+5]": 395,
+    "[Yb+2]": 393,
+    "[Tm+3]": 392,
+    "%32": 392,
+    "[B@@-]": 392,
+    "[B@-]": 387,
+    "[BiH]": 378,
+    "[RuH]": 377,
+    "[RuH+2]": 367,
+    "[Pu]": 366,
+    "[Nb+2]": 365,
+    "[Sb+]": 359,
+    "[P-3]": 331,
+    "[PH]": 329,
+    "[Sb+5]": 321,
+    "[Ga-]": 311,
+    "%37": 310,
+    "[12C]": 295,
+    "[Gd+2]": 288,
+    "[Ta+2]": 286,
+    "[17O]": 284,
+    "%33": 284,
+    "[Si+2]": 282,
+    "[211At]": 278,
+    "[IH]": 276,
+    "[Pm]": 275,
+    "[B+]": 275,
+    "[Cf]": 273,
+    "[64Cu]": 273,
+    "[Zn-2]": 273,
+    "[Li-]": 267,
+    "[Cr+5]": 266,
+    "[Bi+]": 265,
+    "[11CH2]": 260,
+    "[Sn-]": 259,
+    "[Si@@H]": 258,
+    "[GaH2]": 258,
+    "[He]": 258,
+    "%36": 256,
+    "[PbH]": 250,
+    "[99Tc+3]": 247,
+    "[Am]": 241,
+    "%35": 240,
+    "[P-2]": 235,
+    "[SbH2]": 233,
+    "%34": 232,
+    "[Fe-]": 231,
+    "[SeH2]": 228,
+    "[Si@H]": 218,
+    "[Ni+]": 216,
+    "%38": 216,
+    "[InH2]": 214,
+    "[18F-]": 212,
+    "[Es]": 212,
+    "%40": 210,
+    "[Ge+4]": 209,
+    "[Ra]": 204,
+    "[Ir-3]": 203,
+    "%39": 202,
+    "[Pa]": 198,
+    "[NiH2]": 193,
+    "[OH]": 192,
+    "[Mn+]": 192,
+    "%41": 192,
+    "[16OH]": 188,
+    "%43": 184,
+    "[Ir+]": 182,
+    "%42": 182,
+    "[Bk]": 180,
+    "[Th+2]": 179,
+    "[Rh+]": 178,
+    "[35S]": 177,
+    "[Tc+3]": 176,
+    "[3H+]": 173,
+    "[32P]": 171,
+    "[64Cu+2]": 170,
+    "[Os+6]": 167,
+    "[AsH3]": 163,
+    "[16O]": 160,
+    "[PH-2]": 158,
+    "[Zn-]": 157,
+    "[InH]": 151,
+    "[Mg+]": 150,
+    "[Ne]": 150,
+    "%44": 148,
+    "[SbH3]": 143,
+    "[68Ga+3]": 142,
+    "[111In+3]": 140,
+    "[Ru+8]": 135,
+    "[Tl+3]": 134,
+    "[PbH2]": 132,
+    "%45": 132,
+    "[As+3]": 131,
+    "[TlH]": 129,
+    "[XeH]": 127,
+    "[13CH4]": 127,
+    "[18O-]": 121,
+    "[17OH]": 118,
+    "[13C-]": 118,
+    "[Nb+3]": 118,
+    "[Db]": 117,
+    "[InH3]": 117,
+    "[Ru-]": 117,
+    "[77Br]": 116,
+    "[12CH]": 116,
+    "[W+]": 115,
+    "[Mt]": 112,
+    "[11CH]": 112,
+    "[Si+3]": 110,
+    "[ClH]": 107,
+    "[PoH]": 105,
+    "[Tc+5]": 103,
+    "[68Ga]": 100,
+    "[In+]": 100,
+    "[Pt-2]": 98,
+    "[RuH+3]": 96,
+    "[Cu-]": 96,
+    "[SiH+]": 96,
+    "[14N]": 94,
+    "[177Lu]": 91,
+    "[BiH3]": 90,
+    "[IrH+2]": 89,
+    "[Kr]": 88,
+    "[NiH]": 88,
+    "[Mo+]": 87,
+    "[Os+5]": 86,
+    "[AlH2-]": 85,
+    "[TlH2]": 81,
+    "[Au-]": 81,
+    "[OsH]": 80,
+    "[RuH2]": 80,
+    "[RuH+]": 80,
+    "[PdH2]": 79,
+    "[Tc+2]": 78,
+    "[111In]": 77,
+    "[18FH]": 76,
+    "[Hs]": 72,
+    "[Bh]": 72,
+    "%46": 72,
+    "%47": 72,
+    "[12CH3]": 72,
+    "[Rn]": 69,
+    "[Cl]": 69,
+    "[SiH2-]": 69,
+    "[12CH2]": 68,
+    "[AlH2+]": 68,
+    "[99Tc+5]": 64,
+    "[Os+7]": 63,
+    "[35Cl]": 63,
+    "[Pd-2]": 62,
+    "[AlH-]": 62,
+    "%48": 62,
+    "[Tc+6]": 62,
+    "[90Y]": 61,
+    "[Ge-2]": 59,
+    "[P@@H]": 58,
+    "%49": 58,
+    "[PtH]": 57,
+    "[Co-2]": 57,
+    "[P@H]": 57,
+    "[Pd-]": 56,
+    "[Cu-2]": 55,
+    "[Ir-2]": 55,
+    "[177Lu+3]": 55,
+    "[10BH]": 55,
+    "[In-]": 55,
+    "[37Cl]": 55,
+    "[99Tc+7]": 54,
+    "[2H+]": 52,
+    "[Tc+7]": 52,
+    "[16N]": 51,
+    "[Tb+4]": 51,
+    "[34S]": 51,
+    "[AlH4-]": 50,
+    "[Ru-2]": 49,
+    "%51": 48,
+    "%53": 48,
+    "[TeH2]": 47,
+    "[10B-]": 47,
+    "[Ca+]": 46,
+    "[Tc+]": 46,
+    "%55": 46,
+    "[188Re]": 45,
+    "[IrH2]": 44,
+    "%50": 44,
+    "%52": 44,
+    "%54": 44,
+    "[AlH+]": 43,
+    "[Md]": 43,
+    "[Nb-]": 43,
+    "%56": 42,
+    "[CH3]": 41,
+    "[CuH]": 41,
+    "[15NH3]": 40,
+    "[10BH-]": 40,
+    "[Br]": 40,
+    "[14NH]": 38,
+    "[127I]": 38,
+    "[Ge@]": 38,
+    "[14C@@]": 38,
+    "[80Br]": 37,
+    "[SiH2+]": 37,
+    "[125I-]": 36,
+    "[RhH+2]": 35,
+    "[Ti-2]": 35,
+    "[B@@H-]": 35,
+    "[67Ga+3]": 35,
+    "[PbH2+2]": 35,
+    "[B@H-]": 35,
+    "%57": 34,
+    "[15N-]": 34,
+    "[67Cu]": 34,
+    "[Ge@@]": 33,
+    "[SiH3-]": 33,
+    "[13NH2]": 33,
+    "[12C@@H]": 33,
+    "[I]": 32,
+    "[SeH-]": 31,
+    "[ReH]": 31,
+    "[68GaH3]": 30,
+    "[PdH+]": 30,
+    "[15O]": 30,
+    "%58": 30,
+    "%60": 30,
+    "%62": 30,
+    "[225Ac]": 30,
+    "[WH2]": 29,
+    "[AsH2+]": 29,
+    "[Pt-]": 29,
+    "[75Se]": 29,
+    "[7Li+]": 28,
+    "%59": 28,
+    "%61": 28,
+    "[Hg-2]": 28,
+    "[PoH2]": 27,
+    "[RuH2+2]": 27,
+    "[11C-]": 27,
+    "[186Re]": 27,
+    "[ZrH2]": 26,
+    "[RhH]": 26,
+    "[14NH2]": 26,
+    "[6Li+]": 26,
+    "%64": 26,
+    "[OsH2]": 25,
+    "[Hg-]": 25,
+    "[14C-]": 25,
+    "[W-]": 25,
+    "[15NH3+]": 25,
+    "[Ni-2]": 24,
+    "[SeH+]": 24,
+    "[SnH+3]": 24,
+    "[As+5]": 24,
+    "[15NH+]": 24,
+    "[Ni-]": 24,
+    "%63": 24,
+    "[SnH4]": 23,
+    "[Al-3]": 23,
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+    "[62Cu+]": 1,
+    "[64Cu+]": 1,
+    "[61Cu+]": 1,
+    "[37SH2]": 1,
+    "[30Si]": 1,
+    "[28Al]": 1,
+    "[19OH2]": 1,
+    "[8He]": 1,
+    "[6He]": 1,
+    "[153Pm]": 1,
+    "[209Bi]": 1,
+    "[66Zn+2]": 1,
+    "[191Ir]": 1,
+    "[UH3]": 1,
+    "[S@@H]": 1,
+    "[RuH-]": 1,
+    "[ClH3+3]": 1,
+    "[NiH2+2]": 1,
+    "[122Te]": 1,
+    "[156Gd]": 1,
+    "[112Cd]": 1,
+    "[116Sn]": 1,
+    "[120Sn]": 1,
+    "[Sn@@]": 1,
+    "[118Pd+2]": 1,
+    "[118Pd]": 1,
+    "[PtH4]": 1,
+    "[VH2]": 1,
+    "[84Sr]": 1,
+    "[UH2]": 1,
+    "[198Hg]": 1,
+    "[52Mn+2]": 1,
+    "[64Ga]": 1,
+    "[181Ta]": 1,
+    "[BiH+]": 1,
+    "[12NH3]": 1,
+    "[62Ga]": 1,
+    "[39Ar]": 1,
+    "[144Sm]": 1,
+    "[58Fe]": 1,
+    "[153Eu]": 1,
+    "[85Rb]": 1,
+    "[171Yb]": 1,
+    "[172Yb]": 1,
+    "[114Cd]": 1,
+    "[51Fe]": 1,
+    "[142Ce]": 1,
+    "[207Tl]": 1,
+    "[92Mo]": 1,
+    "[115Sn]": 1,
+    "[140Ce]": 1,
+    "[202Hg]": 1,
+    "[180W]": 1,
+    "[182W]": 1,
+    "[183W]": 1,
+    "[184W]": 1,
+    "[96Mo]": 1,
+    "[47Ti]": 1,
+    "[111Cd]": 1,
+    "[143Nd]": 1,
+    "[145Nd]": 1,
+    "[126Te]": 1,
+    "[128Te]": 1,
+    "[130Te]": 1,
+    "[185Re]": 1,
+    "[97Mo]": 1,
+    "[98Mo]": 1,
+    "[183Re]": 1,
+    "[52V]": 1,
+    "[80Se]": 1,
+    "[87Kr]": 1,
+    "[137Xe]": 1,
+    "[196Au]": 1,
+    "[146Ce]": 1,
+    "[88Kr]": 1,
+    "[51Ti]": 1,
+    "[138Xe]": 1,
+    "[37S]": 1,
+    "[38S]": 1,
+    "[30PH3]": 1,
+    "[19CH3]": 1,
+    "[14OH2]": 1,
+    "[17NH4+]": 1,
+    "[32PH2]": 1,
+    "[13B]": 1,
+    "[216Bi]": 1,
+    "[117Sn+2]": 1,
+    "[P@H+]": 1,
+    "[MoH3]": 1,
+    "[186W]": 1,
+    "[FeH4]": 1,
+    "[HgH2]": 1,
+    "[86Tc]": 1,
+    "[141Pr+3]": 1,
+    "[141Pr]": 1,
+    "[Ge@H]": 1,
+    "[204Hg]": 1,
+    "[ThH4]": 1,
+    "[WH6]": 1,
+    "[218AtH]": 1,
+    "[67Zn+2]": 1,
+    "[65Cu+2]": 1,
+    "[110Te]": 1,
+    "[58Fe+3]": 1,
+    "[142Nd]": 1,
+    "[38K]": 1,
+    "[198Au+3]": 1,
+    "[122IH]": 1,
+    "[38PH3]": 1,
+    "[130I-]": 1,
+    "[40K+]": 1,
+    "[38K+]": 1,
+    "[28Mg+2]": 1,
+    "[58Co+3]": 1,
+    "[229Rn]": 1,
+    "[218Pb]": 1,
+    "[167Tm+3]": 1,
+    "[100Tc+5]": 1,
+    "[110Cd]": 1,
+    "[16CH2]": 1,
+    "[100Mo]": 1,
+    "[208Tl+]": 1,
+    "[18CH3]": 1,
+    "[135I]": 1,
+    "[13OH2]": 1,
+    "[192Bi]": 1,
+    "[194Bi]": 1,
+    "[196Bi]": 1,
+    "[161Tb+3]": 1,
+    "[197Hg+2]": 1,
+    "[191Os+4]": 1,
+    "[170Tm+3]": 1,
+    "[233U+4]": 1,
+    "[106Cd]": 1,
+    "[122Sn]": 1,
+    "[132I-]": 1,
+    "[83Sr+2]": 1,
+    "[169Er+3]": 1,
+    "[122I-]": 1,
+    "[120I-]": 1,
+    "[92Sr+2]": 1,
+    "[126I-]": 1,
+    "[126Sb+3]": 1,
+    "[127Sb+3]": 1,
+    "[136Eu+3]": 1,
+    "[136Eu]": 1,
+    "[125Sn+4]": 1,
+    "[175Yb+3]": 1,
+    "[94Tc+7]": 1,
+    "[86Y+3]": 1,
+    "[135I-]": 1,
+    "[15O-2]": 1,
+    "[151Eu+3]": 1,
+    "[28SiH3]": 1,
+    "[35S-]": 1,
+    "[15NH-]": 1,
+    "[91Y+3]": 1,
+    "[106Ru+3]": 1,
+    "[80Br-]": 1,
+    "[CeH3]": 1,
+    "[37ClH]": 1,
+    "[21NH3]": 1,
+    "[18OH3+]": 1,
+    "[17B]": 1,
+    "[RuH5]": 1,
+    "[35S-2]": 1,
+    "[17OH-]": 1,
+    "[212Ra]": 1,
+    "[75Br-]": 1,
+    "[79Br-]": 1,
+    "[113Ag]": 1,
+    "[23Na]": 1,
+    "[34Cl-]": 1,
+    "[34ClH]": 1,
+    "[38Cl-]": 1,
+    "[56Fe]": 1,
+    "[77Br-]": 1,
+    "[90Zr+4]": 1,
+    "[90Zr]": 1,
+    "[102Pd]": 1,
+    "[154Eu+3]": 1,
+    "[57Mn]": 1,
+    "[165Tm]": 1,
+    "[23Na+]": 1,
+    "[27Al+3]": 1,
+    "[31P-3]": 1,
+    "[34S-2]": 1,
+    "[39K+]": 1,
+    "[59Co+3]": 1,
+    "[60Ni+2]": 1,
+    "[75As+3]": 1,
+    "[75As+5]": 1,
+    "[82Se-2]": 1,
+    "[82Se+4]": 1,
+    "[82Se+6]": 1,
+    "[88Sr+2]": 1,
+    "[111Cd+2]": 1,
+    "[107Ag]": 1,
+    "[12CH-]": 1,
+    "[12N+]": 1,
+    "[Se@@H]": 1,
+    "[BiH4]": 1,
+    "[203Pb+2]": 1,
+    "[68Ge+4]": 1,
+    "[44Sc+3]": 1,
+    "[89Zr+3]": 1,
+    "[55Mn]": 1,
+    "[75As]": 1,
+    "[152Dy]": 1,
+    "[217At]": 1,
+    "[AsH5]": 1,
+    "[TeH+]": 1,
+    "[151Eu]": 1,
+    "[103Rh]": 1,
+    "[124Xe]": 1,
+    "[152Tb]": 1,
+    "[20Ne]": 1,
+    "[52Fe]": 1,
+    "[94Zr+4]": 1,
+    "[94Zr]": 1,
+    "[149Pr]": 1,
+    "[53Cr+6]": 1,
+    "[53Cr]": 1,
+    "[81Br-]": 1,
+    "[112Pd]": 1,
+    "[125Xe]": 1,
+    "[155Gd]": 1,
+    "[157Gd]": 1,
+    "[168Yb]": 1,
+    "[184Os]": 1,
+    "[166Tb]": 1,
+    "[221Fr]": 1,
+}
+
+CID_SMILES_ALPHABET = list(CID_SMILES_COUNTS.keys())
+
+ZINC_250K_SMILES_COUNTS = {
+    "": 8894435,
+    "C": 4034842,
+    "=": 1580410,
+    "(": 966950,
+    ")": 966950,
+    "1": 717220,
+    "N": 626877,
+    "O": 551937,
+    "2": 458888,
+    "3": 163222,
+    "[C@@H]": 105871,
+    "[C@H]": 100551,
+    "S": 100291,
+    "F": 79430,
+    "Cl": 42872,
+    "[NH+]": 40289,
+    "4": 30516,
+    "[O-]": 24276,
+    "[NH2+]": 17571,
+    "Br": 12722,
+    "[N+]": 12139,
+    "[C@]": 7085,
+    "[NH3+]": 6788,
+    "[C@@]": 6519,
+    "5": 2492,
+    "[N-]": 1527,
+    "[S@]": 1082,
+    "[S@@]": 1054,
+    "I": 888,
+    "[S-]": 446,
+    "6": 84,
+    "P": 69,
+    "[P@@]": 30,
+    "[P@]": 23,
+    "[O+]": 13,
+    "[NH-]": 12,
+    "7": 8,
+    "[OH+]": 5,
+    "[S+]": 3,
+    "[CH-]": 2,
+    "[SH+]": 2,
+    "8": 2,
+    "[P@@H]": 1,
+    "[PH2]": 1,
+    "[P+]": 1,
+    "[CH2-]": 1,
+    "[PH+]": 1,
+    "[PH]": 1,
+    "[S@@+]": 1,
+}
+
+ZINC_250K_SMILES_ALPHABET = list(ZINC_250K_SMILES_COUNTS.keys())
diff --git a/src/poli/core/util/tokenizers/__init__.py b/src/poli/core/util/tokenizers/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/poli/core/util/tokenizers/abstract_tokenizer.py b/src/poli/core/util/tokenizers/abstract_tokenizer.py
new file mode 100644
index 00000000..217059a6
--- /dev/null
+++ b/src/poli/core/util/tokenizers/abstract_tokenizer.py
@@ -0,0 +1,49 @@
+from __future__ import annotations
+
+import numpy as np
+
+
+def _pad(
+    texts: list[list[str]], max_sequence_length: int, padding_token: str = ""
+) -> list[list[str]]:
+    if max_sequence_length < max(map(len, texts)):
+        raise ValueError(
+            f"max_sequence_length ({max_sequence_length}) must be greater than the length of the longest text ({max(map(len, texts))})"
+        )
+    return [
+        text + [padding_token] * (max_sequence_length - len(text)) for text in texts
+    ]
+
+
+class AbstractTokenizer:
+    def __init__(
+        self, max_sequence_length: int | float | None = None, padding_token: str = ""
+    ) -> None:
+        if isinstance(max_sequence_length, float):
+            assert (
+                max_sequence_length == np.inf
+            ), "max_sequence_length must be np.inf if float"
+
+        self.max_sequence_length = max_sequence_length
+        self.padding_token = padding_token
+
+    def _tokenize(self, texts: str | list[str]) -> list[str] | list[list[str]]:
+        raise NotImplementedError
+
+    def tokenize(self, texts: str | list[str]) -> np.ndarray:
+        unpadded_tokens = self._tokenize(texts)
+
+        if isinstance(unpadded_tokens[0], list):
+            tokens = unpadded_tokens
+        else:
+            tokens = [unpadded_tokens]
+
+        if self.max_sequence_length is None or np.isinf(self.max_sequence_length):
+            max_length = max(map(len, tokens))
+            tokens = _pad(tokens, max_length, padding_token=self.padding_token)
+        else:
+            tokens = _pad(
+                tokens, self.max_sequence_length, padding_token=self.padding_token
+            )
+
+        return np.array(tokens)
diff --git a/src/poli/core/util/tokenizers/character_tokenizer.py b/src/poli/core/util/tokenizers/character_tokenizer.py
new file mode 100644
index 00000000..b0148209
--- /dev/null
+++ b/src/poli/core/util/tokenizers/character_tokenizer.py
@@ -0,0 +1,13 @@
+from __future__ import annotations
+
+from poli.core.util.tokenizers.abstract_tokenizer import AbstractTokenizer
+
+
+class CharacterTokenizer(AbstractTokenizer):
+    def _tokenize(self, texts: str | list[str]) -> list[str] | list[list[str]]:
+        if isinstance(texts, str):
+            return list(texts)
+        elif isinstance(texts, list):
+            return [list(t) for t in texts]
+        else:
+            raise ValueError(f"Expected str or list, got {type(texts)}")
diff --git a/src/poli/core/util/tokenizers/selfies_tokenizer.py b/src/poli/core/util/tokenizers/selfies_tokenizer.py
new file mode 100644
index 00000000..63ecacce
--- /dev/null
+++ b/src/poli/core/util/tokenizers/selfies_tokenizer.py
@@ -0,0 +1,22 @@
+from __future__ import annotations
+
+import selfies as sf
+
+from poli.core.util.tokenizers.abstract_tokenizer import AbstractTokenizer
+
+
+class SELFIESTokenizer(AbstractTokenizer):
+    def __init__(
+        self,
+        max_sequence_length: int | float | None = None,
+        padding_token: str = "[nop]",
+    ) -> None:
+        super().__init__(max_sequence_length, padding_token)
+
+    def _tokenize(self, texts: str | list[str]) -> list[str] | list[list[str]]:
+        if isinstance(texts, str):
+            return list(sf.split_selfies(texts))
+        elif isinstance(texts, list):
+            return [list(sf.split_selfies(t)) for t in texts]
+        else:
+            raise ValueError(f"Expected str or list, got {type(texts)}")
diff --git a/src/poli/core/util/tokenizers/smiles_tokenizer.py b/src/poli/core/util/tokenizers/smiles_tokenizer.py
new file mode 100644
index 00000000..910df152
--- /dev/null
+++ b/src/poli/core/util/tokenizers/smiles_tokenizer.py
@@ -0,0 +1,35 @@
+from __future__ import annotations
+
+import re
+
+from poli.core.util.tokenizers.abstract_tokenizer import AbstractTokenizer
+
+
+class SMILESTokenizer(AbstractTokenizer):
+    def __init__(
+        self, max_sequence_length: int | float | None = None, padding_token: str = ""
+    ) -> None:
+        """Tokenizer for SMILES strings, based on DeepChem's basic SMILES tokenizer."""
+        # DeepChem's SMILES tokenizer
+        SMI_REGEX_PATTERN = r"""(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|\#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""
+
+        self.REGEX_FOR_SMILES = re.compile(SMI_REGEX_PATTERN)
+        super().__init__(max_sequence_length, padding_token)
+
+    def _tokenize(self, texts: str | list[str]) -> list[str] | list[list[str]]:
+        smiles = texts
+        if isinstance(smiles, str):
+            smiles = [smiles]
+
+        tokens = [list(self.REGEX_FOR_SMILES.findall(smile)) for smile in smiles]
+
+        # Make sure they all have the same length
+        max_len = max(len(token) for token in tokens)
+
+        for token in tokens:
+            token += [""] * (max_len - len(token))
+
+        if len(tokens) == 1:
+            return tokens[0]
+
+        return tokens
diff --git a/src/poli/tests/tokenizers/__init__.py b/src/poli/tests/tokenizers/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/poli/tests/tokenizers/test_character_tokenizer.py b/src/poli/tests/tokenizers/test_character_tokenizer.py
new file mode 100644
index 00000000..3be9f8c5
--- /dev/null
+++ b/src/poli/tests/tokenizers/test_character_tokenizer.py
@@ -0,0 +1,65 @@
+import numpy as np
+import pytest
+
+from poli.core.util.proteins.defaults import AMINO_ACIDS
+from poli.core.util.tokenizers.character_tokenizer import CharacterTokenizer
+
+
+def test_character_tokenizer_on_single_sequence():
+    one_amino_acid = AMINO_ACIDS[0]
+
+    text = one_amino_acid * 10
+
+    tokenizer = CharacterTokenizer(max_sequence_length=10)
+
+    tokens = tokenizer.tokenize(text)
+    assert (tokens == np.array(list(one_amino_acid * 10))).all()
+
+
+def test_character_tokenizer_on_multiple_sequences_of_same_length():
+    one_amino_acid = AMINO_ACIDS[0]
+
+    texts = [one_amino_acid * 10] * 5
+
+    tokenizer = CharacterTokenizer(max_sequence_length=10)
+
+    tokens = tokenizer.tokenize(texts)
+    assert (tokens == np.array([list(one_amino_acid * 10)] * 5)).all()
+
+
+@pytest.mark.parametrize("max_sequence_length", [np.inf, 15, None])
+def test_character_tokenizer_on_multiple_sequences_of_varying_length(
+    max_sequence_length,
+):
+    one_amino_acid = AMINO_ACIDS[0]
+
+    texts = [
+        one_amino_acid * 10,
+        one_amino_acid * 5,
+        one_amino_acid * 15,
+        one_amino_acid * 3,
+        one_amino_acid * 8,
+    ]
+
+    tokenizer = CharacterTokenizer(max_sequence_length=max_sequence_length)
+
+    tokens = tokenizer.tokenize(texts)
+    assert tokens.shape == (5, 15)
+    assert tokens[0, 11] == tokenizer.padding_token
+
+
+def test_character_tokenizer_outputs_error_on_wrong_max_sequence():
+    one_amino_acid = AMINO_ACIDS[0]
+
+    texts = [
+        one_amino_acid * 10,
+        one_amino_acid * 5,
+        one_amino_acid * 15,
+        one_amino_acid * 3,
+        one_amino_acid * 8,
+    ]
+
+    tokenizer = CharacterTokenizer(max_sequence_length=10)
+
+    with pytest.raises(ValueError):
+        _ = tokenizer.tokenize(texts)
diff --git a/src/poli/tests/tokenizers/test_smiles_and_selfies_tokenizer.py b/src/poli/tests/tokenizers/test_smiles_and_selfies_tokenizer.py
new file mode 100644
index 00000000..6cf58fbc
--- /dev/null
+++ b/src/poli/tests/tokenizers/test_smiles_and_selfies_tokenizer.py
@@ -0,0 +1,69 @@
+from __future__ import annotations
+
+import numpy as np
+import pytest
+
+from poli.core.util.tokenizers.selfies_tokenizer import SELFIESTokenizer
+from poli.core.util.tokenizers.smiles_tokenizer import SMILESTokenizer
+
+
+@pytest.mark.parametrize(
+    "smile, expected_tokens",
+    [
+        ("CCO", ["C", "C", "O"]),
+        ("C1=CC=CC=C1", ["C", "1", "=", "C", "C", "=", "C", "C", "=", "C", "1"]),
+        # TODO: add more
+    ],
+)
+def test_smiles_tokenizer_on_single_sequence(smile: str, expected_tokens: list[str]):
+    tokenizer = SMILESTokenizer(max_sequence_length=np.inf)
+
+    tokens = tokenizer.tokenize(smile)
+    assert (tokens == np.array(expected_tokens)).all()
+
+
+@pytest.mark.parametrize(
+    "selfie, expected_tokens",
+    [
+        ("[C][C][O]", ["[C]", "[C]", "[O]"]),
+        (
+            "[C][=C][C][=C][C][=C][Ring1][=Branch1]",
+            ["[C]", "[=C]", "[C]", "[=C]", "[C]", "[=C]", "[Ring1]", "[=Branch1]"],
+        ),
+    ],
+)
+def test_selfies_tokenizer_on_single_sequence(selfie: str, expected_tokens: list[str]):
+    tokenizer = SELFIESTokenizer(max_sequence_length=np.inf)
+
+    tokens = tokenizer.tokenize(selfie)
+    assert (tokens == np.array(expected_tokens)).all()
+
+
+def test_smiles_on_sequences_of_varying_length():
+    smiles = [
+        "CCO",
+        "C1=CC=CC=C1",
+        "CC(C)C",
+        "CC(C)(C)C",
+        "CC(C)(C)C",
+    ]
+
+    tokenizer = SMILESTokenizer(max_sequence_length=np.inf)
+
+    tokens = tokenizer.tokenize(smiles)
+    assert tokens.shape == (5, 11)
+    assert tokens[0, 3] == tokenizer.padding_token
+    assert tokens[4, 9] == tokenizer.padding_token
+
+
+def test_selfies_on_sequences_of_varying_length():
+    selfies = [
+        "[C][C][O]",
+        "[C][=C][C][=C][C][=C][Ring1][=Branch1]",
+    ]
+
+    tokenizer = SELFIESTokenizer(max_sequence_length=np.inf)
+
+    tokens = tokenizer.tokenize(selfies)
+    assert tokens.shape == (2, 8)
+    assert tokens[0, 4] == tokenizer.padding_token