#!/usr/bin/env python
"""Definitions and properties of amino-acids for p2smi"""

# Natural Amino-acids:

specific_aminos = {
    "Fmoc-Aib-OH": {
        "Code": "Aib",
        "Formula": "C28H29NO5",
        "Letter": "Ŷ",
        "MolWeight": 221.141578848,
        "SMILES": "CC(C)(N)C(=O)O",
        "cterm": "NC(C)(C)C(=O)[*:2]",
        "disulphide": False,
        "ester": False,
        "nterm": "[*:1]NC(C)(C)C(=O)O",
    },
    "Fmoc-Asp(OtBu)-(Dmb)Gly-OH": {
        "Code": "Dtg",
        "Formula": "C28H29NO5",
        "Letter": "Ĝ",
        "MolWeight": 221.141578848,
        "SMILES": "N[C@@H](CC(=O)OC(C)(C)C)C(=O)N(CC1=C(C=C(C=C1)OC)OC)CC(=O)O",
        "nterm": "[*:1]N[C@@H](CC(=O)OC(C)(C)C)C(=O)N(CC1=C(C=C(C=C1)OC)OC)CC(=O)O",  
        "cterm": "N[C@@H](CC(=O)OC(C)(C)C)C(=O)N(CC1=C(C=C(C=C1)OC)OC)CC(=O)[*:2]",
        "disulphide": False,
        "ester": False,
    },
    "Fmoc-Cys(Mmt)-OH": {
        "Code": "Cmt",
        "Formula": "C28H29NO5",
        "Letter": "Ĉ",
        "MolWeight": 221.141578848,
        "SMILES": "COC1=CC=C(C=C1)C(C2=CC=CC=C2)(C3=CC=CC=C3)SC[C@@H](N)C(=O)O",
        "nterm": "N([*:1])[C@@H](CSC(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=C(OC)C=C3)C(=O)O",
        "cterm": "N[C@@H](CSC(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=C(OC)C=C3)C(=O)[*:2]",
        "disulphide": False,
        "ester": False,
    },
    "Fmoc-Glu(OAll)-OH": {
        "Code": "Eal",
        "Formula": "C28H29NO5",
        "Letter": "Ė",
        "MolWeight": 221.141578848,
        "SMILES": "C=CCOC(=O)CC[C@@H](N)C(=O)O",
        "nterm": "[*:1]N[C@@H](CCC(=O)OCC=C)C(=O)O",
        "cterm": "N[C@@H](CCC(=O)OCC=C)C(=O)[*:2]",
        "disulphide": False,
        "ester": False,
    },
    "Fmoc-Lys(palmitoyl-Glu-OtBu)-OH": {
        "Code": "Kpg",
        "Formula": "C28H29NO5",
        "Letter": "Ƙ",
        "MolWeight": 221.141578848,
        "SMILES": "N[C@@H](CCCNC(=O)CCC[C@@H](NC(=O)CCCCCCCCCCCCCCCC)C(=O)OC(C)(C)C)C(=O)O",
        "nterm": "[*:1]N[C@@H](CCCN(C(=O)CCC[C@@H](NC(=O)CCCCCCCCCCCCCCCC)C(=O)OC(C)(C)C))C(=O)O",
        "cterm": "N[C@@H](CCCN(C(=O)CCC[C@@H](NC(=O)CCCCCCCCCCCCCCCC)C(=O)OC(C)(C)C))C(=O)[*:2]",
        "disulphide": False,
        "ester": False,
    },
    "Fmoc-Thr(PO(OBzl)OH)-OH": {
        "Code": "Tpb",
        "Formula": "C28H29NO5",
        "Letter": "Ṯ",
        "MolWeight": 221.141578848,
        "SMILES": "N[C@@H]([C@H](C)OP(=O)(O)OCc1ccccc1)C(=O)O",
        "disulphide": False,
        "ester": False,
        "nterm": "[*:1]N[C@@H]([C@H](C)OP(=O)(O)OCC1=CC=CC=C1)C(=O)O",
        "cterm": "N[C@@H]([C@H](C)OP(=O)(O)OCC1=CC=CC=C1)C(=O)[*:2]"
    },
    "Fmoc-Cycloleucine": {
        "Code": "Cyl",
        "Formula": "C28H29NO5",
        "Letter": "Ċ",
        "MolWeight": 221.141578848,
        "SMILES": "NC1(CCCC1)C(=O)O",
        "nterm": "[*:1]NC1(CCCC1)C(=O)O",
        "cterm": "NC1(CCCC1)C(=O)[*:2]",
        "disulphide": False,
        "ester": False,
    },
    "Fmoc-N-Me-Ala-OH": {
        "Code": "Nma",
        "Formula": "C28H29NO5",
        "Letter": "Ṃ",
        "MolWeight": 221.141578848,
        "SMILES": "CN([C@@H](C)C(=O)O)",
        "cterm": "N(C)[C@@H](C)C(=O)[*:2]",
        "disulphide": False,
        "ester": False,
        "nterm": "[*:1]N(C)[C@@H](C)C(=O)O",
    },
    "Fmoc-N-Me-Leu-OH": {
        "Code": "Nml",
        "Formula": "C28H29NO5",
        "Letter": "Ŀ",
        "MolWeight": 221.141578848,
        "SMILES": "CN([C@@H](CC(C)C))C(=O)O",
        "cterm": "CN([C@@H](CC(C)C)C(=O))[*:2]",
        "disulphide": False,
        "ester": False,
        "nterm": "[*:1]N(C)[C@@H](CC(C)C)C(=O)O",
    },
    "Fmoc-Nle-OH": {
        "Code": "Nle",
        "Formula": "C28H29NO5",
        "Letter": "Ł",
        "MolWeight": 221.141578848,
        "SMILES": "N[C@@H](CCCC)C(=O)O",
        "nterm": "[*:1]N[C@@H](CCCC)C(=O)O",
        "cterm": "N[C@@H](CCCC)C(=O)[*:2]",
        "disulphide": False,
        "ester": False,
    },
    "N-Fmoc-L-homophenylalanine": {
        "Code": "Hph",
        "Formula": "C28H29NO5",
        "Letter": "Ĥ",
        "MolWeight": 221.141578848,
        "SMILES": "N[C@@H](CCC1=CC=CC=C1)C(=O)O",
        "nterm": "[*:1]N[C@@H](CCC1=CC=CC=C1)C(=O)O",
        "cterm": "N[C@@H](CCC1=CC=CC=C1)C(=O)[*:2]",
        "disulphide": False,
        "ester": False,
    },
    "Glycine": {
        "Code": "Gly",
        "Formula": "C2H5NO2",
        "Letter": "G",
        "MolWeight": "75.07",
        "SMILES": "NCC(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Alanine": {
        "Code": "Ala",
        "Formula": "C3H7NO2",
        "Letter": "A",
        "MolWeight": "89.09",
        "SMILES": "N[C@@H](C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Arginine": {
        "Code": "Arg",
        "Formula": "C6H14N4O2",
        "Letter": "R",
        "MolWeight": "174.20",
        "SMILES": "N[C@@H](CCCNC(=N)N)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": "N[C@@H](CCCNC(=N*)N)C(=O)O",
    },
    "L-Asparagine": {
        "Code": "Asn",
        "Formula": "C4H8N2O3",
        "Letter": "N",
        "MolWeight": "132.12",
        "SMILES": "N[C@@H](CC(=O)N)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": "N[C@@H](CC(=O)N*)C(=O)O",
    },
    "L-Aspartic_Acid": {
        "Code": "Asp",
        "Formula": "C4H7NO4",
        "Letter": "D",
        "MolWeight": "133.10",
        "SMILES": "N[C@@H](CC(=O)O)C(=O)O",
        "cterm": "N[C@@H](CC*(=O))C(=O)O",
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Cysteine": {
        "Code": "Cys",
        "Formula": "C3H7NO2S",
        "Letter": "C",
        "MolWeight": "121.16",
        "SMILES": "N[C@@H](CS)C(=O)O",
        "cterm": False,
        "disulphide": "N[C@@H](CS*)C(=O)O",
        "ester": False,
        "nterm": False,
    },
    "L-Glutamic_Acid": {
        "Code": "Glu",
        "Formula": "C5H9NO4",
        "Letter": "E",
        "MolWeight": "147.13",
        "SMILES": "N[C@@H](CCC(=O)O)C(=O)O",
        "cterm": "N[C@@H](CCC*(=O))C(=O)O",
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Glutamine": {
        "Code": "Gln",
        "Formula": "C5H10N2O3",
        "Letter": "Q",
        "MolWeight": "146.15",
        "SMILES": "N[C@@H](CCC(=O)N)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": "N[C@@H](CCC(=O)N*)C(=O)O",
    },
    "L-Histidine": {
        "Code": "His",
        "Formula": "C6H9N3O2",
        "Letter": "H",
        "MolWeight": "155.16",
        "SMILES": "N[C@@H](CC1=CNC=N1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Isoleucine": {
        "Code": "Ile",
        "Formula": "C6H13NO2",
        "Letter": "I",
        "MolWeight": "131.18",
        "SMILES": "N[C@@H]([C@H](CC)C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Leucine": {
        "Code": "Leu",
        "Formula": "C6H13NO2",
        "Letter": "L",
        "MolWeight": "131.18",
        "SMILES": "N[C@@H](CC(C)C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Lysine": {
        "Code": "Lys",
        "Formula": "C6H12N2O2",
        "Letter": "K",
        "MolWeight": "146.19",
        "SMILES": "N[C@@H](CCCCN)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": "N[C@@H](CCCCN*)C(=O)O",
    },
    "L-Methionine": {
        "Code": "Met",
        "Formula": "C5H11NO2S",
        "Letter": "M",
        "MolWeight": "149.21",
        "SMILES": "N[C@@H](CCSC)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Phenylalanine": {
        "Code": "Phe",
        "Formula": "C9H11NO2",
        "Letter": "F",
        "MolWeight": "165.19",
        "SMILES": "N[C@@H](Cc1ccccc1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Proline": {
        "Code": "Pro",
        "Formula": "C5H9NO2",
        "Letter": "P",
        "MolWeight": "115.13",
        "SMILES": "N1[C@@H](CCC1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Serine": {
        "Code": "Ser",
        "Formula": "C3H7NO2",
        "Letter": "S",
        "MolWeight": "105.09",
        "SMILES": "N[C@@H](CO)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": "N[C@@H](CO*)C(=O)O",
        "nterm": False,
    },
    "L-Threonine": {
        "Code": "Thr",
        "Formula": "C4H9NO3",
        "Letter": "T",
        "MolWeight": "119.12",
        "SMILES": "N[C@@H]([C@H](O)C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": "N[C@@H]([C@H](O*)C)C(=O)O",
        "nterm": False,
    },
    "L-Tryptophan": {
        "Code": "Trp",
        "Formula": "C11H12N2O2",
        "Letter": "W",
        "MolWeight": "204.23",
        "SMILES": "N[C@@H](CC(=CN2)C1=C2C=CC=C1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "L-Tyrosine": {
        "Code": "Tyr",
        "Formula": "C9H11NO3",
        "Letter": "Y",
        "MolWeight": "181.19",
        "SMILES": "N[C@@H](Cc1ccc(O)cc1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": "N[C@@H](Cc1ccc(O*)cc1)C(=O)O",
        "nterm": False,
    },
    "L-Valine": {
        "Code": "Val",
        "Formula": "C5H11NO2",
        "Letter": "V",
        "MolWeight": "117.15",
        "SMILES": "N[C@@H](C(C)C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Alanine": {
        "Code": "ala",
        "Formula": "C3H7NO2",
        "Letter": "a",
        "MolWeight": "89.09",
        "SMILES": "N[C@H](C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Arginine": {
        "Code": "arg",
        "Formula": "C6H14N4O2",
        "Letter": "r",
        "MolWeight": "174.20",
        "SMILES": "N[C@H](CCCNC(=N)N)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": "N[C@H](CCCNC(=N*)N)C(=O)O",
    },
    "D-Asparagine": {
        "Code": "asn",
        "Formula": "C4H8N2O3",
        "Letter": "n",
        "MolWeight": "132.12",
        "SMILES": "N[C@H](CC(=O)N)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": "N[C@H](CC(=O)N*)C(=O)O",
    },
    "D-Aspartic_Acid": {
        "Code": "asp",
        "Formula": "C4H7NO4",
        "Letter": "d",
        "MolWeight": "133.10",
        "SMILES": "N[C@H](CC(=O)O)C(=O)O",
        "cterm": "N[C@H](CC*(=O))C(=O)O",
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Cysteine": {
        "Code": "cys",
        "Formula": "C3H7NO2S",
        "Letter": "c",
        "MolWeight": "121.16",
        "SMILES": "N[C@H](CS)C(=O)O",
        "cterm": False,
        "disulphide": "N[C@H](CS*)C(=O)O",
        "ester": False,
        "nterm": False,
    },
    "D-Glutamic_Acid": {
        "Code": "glu",
        "Formula": "C5H9NO4",
        "Letter": "e",
        "MolWeight": "147.13",
        "SMILES": "N[C@H](CCC(=O)O)C(=O)O",
        "cterm": "N[C@H](CCC*(=O))C(=O)O",
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Glutamine": {
        "Code": "gln",
        "Formula": "C5H10N2O3",
        "Letter": "q",
        "MolWeight": "146.15",
        "SMILES": "N[C@H](CCC(=O)N)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": "N[C@H](CCC(=O)N*)C(=O)O",
    },
    "D-Histidine": {
        "Code": "his",
        "Formula": "C6H9N3O2",
        "Letter": "h",
        "MolWeight": "155.16",
        "SMILES": "N[C@H](CC1=CNC=N1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Isoleucine": {
        "Code": "ile",
        "Formula": "C6H13NO2",
        "Letter": "i",
        "MolWeight": "131.18",
        "SMILES": "N[C@H]([C@@H](CC)C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Leucine": {
        "Code": "leu",
        "Formula": "C6H13NO2",
        "Letter": "l",
        "MolWeight": "131.18",
        "SMILES": "N[C@H](CC(C)C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Lysine": {
        "Code": "lys",
        "Formula": "C6H12N2O2",
        "Letter": "k",
        "MolWeight": "146.19",
        "SMILES": "N[C@H](CCCCN)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": "N[C@H](CCCCN*)C(=O)O",
    },
    "D-Methionine": {
        "Code": "met",
        "Formula": "C5H11NO2S",
        "Letter": "m",
        "MolWeight": "149.21",
        "SMILES": "N[C@H](CCSC)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Phenylalanine": {
        "Code": "phe",
        "Formula": "C9H11NO2",
        "Letter": "f",
        "MolWeight": "165.19",
        "SMILES": "N[C@H](Cc1ccccc1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Proline": {
        "Code": "pro",
        "Formula": "C5H9NO2",
        "Letter": "p",
        "MolWeight": "115.13",
        "SMILES": "N1[C@H](CCC1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Serine": {
        "Code": "ser",
        "Formula": "C3H7NO2",
        "Letter": "s",
        "MolWeight": "105.09",
        "SMILES": "N[C@H](CO)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": "N[C@H](CO*)C(=O)O",
        "nterm": False,
    },
    "D-Tryptophan": {
        "Code": "trp",
        "Formula": "C11H12N2O2",
        "Letter": "w",
        "MolWeight": "204.23",
        "SMILES": "N[C@H](CC(=CN2)C1=C2C=CC=C1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Tyrosine": {
        "Code": "tyr",
        "Formula": "C9H11NO3",
        "Letter": "y",
        "MolWeight": "181.19",
        "SMILES": "N[C@H](Cc1ccc(O)cc1)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": "N[C@H](Cc1ccc(O*)cc1)C(=O)O",
        "nterm": False,
    },
    "D-Valine": {
        "Code": "val",
        "Formula": "C5H11NO2",
        "Letter": "v",
        "MolWeight": "117.15",
        "SMILES": "N[C@H](C(C)C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": False,
        "nterm": False,
    },
    "D-Threonine": {
        "Code": "thr",
        "Formula": "C4H9NO3",
        "Letter": "t",
        "MolWeight": "119.12",
        "SMILES": "N[C@H]([C@@H](O)C)C(=O)O",
        "cterm": False,
        "disulphide": False,
        "ester": "N[C@H]([C@@H](O*)C)C(=O)O",
        "nterm": False,
    },
}