ThreeLetterResidues.jl

# Three letters (for PDB and MSA)
# ===============================

# download("ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif","components.cif")
#
# open("components.cif","r") do fh
#     m3 = nothing
#     m1 = nothing
#     peptide = false
#     for line in eachline(fh)
#         if startswith(line, "_chem_comp")
#             if m3 == nothing
#                 m3 = match(r"^_chem_comp.three_letter_code\s+(\w{3})\s*$",line) # It avoids: DA, DT, ...
#             end
#             if m1 == nothing
#                 m1 = match(r"^_chem_comp.one_letter_code\s+(\w{1})\s*$",line) # It avoids: ?
#             end
#             if startswith(line,"_chem_comp.type")
#                 peptide = occursin(r"peptide"i,line) # It avoids 0DA, 2DA, etc...
#             end
#             if m1 != nothing && m3 != nothing && parent != nothing && peptide
#                 res = collect(m1[1])[1]
#                 if (Residue(res) != XAA) # It avoids non standar residues, i.e. PYL
#                     println("\"$(m3[1])\" => '$(Char(Residue(res)))',")
#                 end
#                 m3 = nothing
#                 m1 = nothing
#                 peptide = false
#             end
#         else
#             m3 = nothing
#             m1 = nothing
#             peptide = false
#         end
#     end
# end

"""
`THREE2ONE` is a dictionary that maps three-letter amino acid residue codes (`String`)
to their corresponding one-letter codes (`Char`). The dictionary is generated by
parsing `components.cif` file from the Protein Data Bank.

```jldoctest
julia> using MIToS.Utils

julia> one_letter_code = THREE2ONE["ALA"]
'A': ASCII/Unicode U+0041 (category Lu: Letter, uppercase)
```
"""
const THREE2ONE = Dict{String,Char}(
    "00C" => 'C',
    "02K" => 'A',
    "02L" => 'N',
    "03Y" => 'C',
    "07O" => 'C',
    "08P" => 'C',
    "0A0" => 'D',
    "0A1" => 'Y',
    "0A2" => 'K',
    "0A8" => 'C',
    "0AA" => 'V',
    "0AB" => 'V',
    "0AC" => 'G',
    "0AF" => 'W',
    "0AG" => 'L',
    "0AH" => 'S',
    "0AK" => 'D',
    "0BN" => 'F',
    "0CS" => 'A',
    "0E5" => 'T',
    "0EA" => 'Y',
    "0FL" => 'A',
    "0NC" => 'A',
    "0WZ" => 'Y',
    "0Y8" => 'P',
    "143" => 'C',
    "1OP" => 'Y',
    "1PA" => 'F',
    "1PI" => 'A',
    "1TQ" => 'W',
    "1TY" => 'Y',
    "1X6" => 'S',
    "200" => 'F',
    "23F" => 'F',
    "26B" => 'T',
    "2AG" => 'A',
    "2CO" => 'C',
    "2FM" => 'M',
    "2HF" => 'H',
    "2KK" => 'K',
    "2KP" => 'K',
    "2LU" => 'L',
    "2ML" => 'L',
    "2MR" => 'R',
    "2MT" => 'P',
    "2OR" => 'R',
    "2QZ" => 'T',
    "2R3" => 'Y',
    "2TL" => 'T',
    "2TY" => 'Y',
    "2VA" => 'V',
    "2XA" => 'C',
    "33X" => 'A',
    "3AH" => 'H',
    "3CF" => 'F',
    "3GA" => 'A',
    "3MD" => 'D',
    "3NF" => 'Y',
    "3QN" => 'K',
    "3XH" => 'G',
    "4BF" => 'Y',
    "4CF" => 'F',
    "4CY" => 'M',
    "4DP" => 'W',
    "4FB" => 'P',
    "4FW" => 'W',
    "4GJ" => 'C',
    "4HT" => 'W',
    "4IN" => 'W',
    "4PH" => 'F',
    "4U7" => 'A',
    "56A" => 'H',
    "5AB" => 'A',
    "5CR" => 'F',
    "5CS" => 'C',
    "5CT" => 'K',
    "5CW" => 'W',
    "5HP" => 'E',
    "5OW" => 'K',
    "5VV" => 'N',
    "6CL" => 'K',
    "6CW" => 'W',
    "6GL" => 'A',
    "6HN" => 'K',
    "6V1" => 'C',
    "6WK" => 'C',
    "7JA" => 'I',
    "9NE" => 'E',
    "9NF" => 'F',
    "9NR" => 'R',
    "9NV" => 'V',
    "A5N" => 'N',
    "AA3" => 'A',
    "AA4" => 'A',
    "AAR" => 'R',
    "ABA" => 'A',
    "ACB" => 'D',
    "ACL" => 'R',
    "AEI" => 'D',
    "AFA" => 'N',
    "AGM" => 'R',
    "AGT" => 'C',
    "AHB" => 'N',
    "AHO" => 'A',
    "AHP" => 'A',
    "AIB" => 'A',
    "AKL" => 'D',
    "AKZ" => 'D',
    "ALA" => 'A',
    "ALC" => 'A',
    "ALM" => 'A',
    "ALN" => 'A',
    "ALO" => 'T',
    "ALS" => 'A',
    "ALT" => 'A',
    "ALV" => 'A',
    "ALY" => 'K',
    "AN8" => 'A',
    "APH" => 'A',
    "API" => 'K',
    "APK" => 'K',
    "AR2" => 'R',
    "AR4" => 'E',
    "AR7" => 'R',
    "ARG" => 'R',
    "ARM" => 'R',
    "ARO" => 'R',
    "AS2" => 'D',
    "ASA" => 'D',
    "ASB" => 'D',
    "ASI" => 'D',
    "ASK" => 'D',
    "ASL" => 'D',
    "ASN" => 'N',
    "ASP" => 'D',
    "ASQ" => 'D',
    "AYA" => 'A',
    "AZK" => 'K',
    "AZS" => 'S',
    "AZY" => 'Y',
    "B1F" => 'F',
    "B2A" => 'A',
    "B2F" => 'F',
    "B2I" => 'I',
    "B2V" => 'V',
    "B3A" => 'A',
    "B3D" => 'D',
    "B3E" => 'E',
    "B3K" => 'K',
    "B3S" => 'S',
    "B3U" => 'H',
    "B3X" => 'N',
    "B3Y" => 'Y',
    "BB6" => 'C',
    "BB7" => 'C',
    "BB8" => 'F',
    "BB9" => 'C',
    "BBC" => 'C',
    "BCS" => 'C',
    "BFD" => 'D',
    "BG1" => 'S',
    "BH2" => 'D',
    "BHD" => 'D',
    "BIF" => 'F',
    "BIU" => 'I',
    "BL2" => 'L',
    "BLE" => 'L',
    "BLY" => 'K',
    "BMT" => 'T',
    "BNN" => 'F',
    "BOR" => 'R',
    "BPE" => 'C',
    "BSE" => 'S',
    "BTA" => 'L',
    "BTC" => 'C',
    "BTR" => 'W',
    "BUC" => 'C',
    "BUG" => 'V',
    "C1X" => 'K',
    "C22" => 'A',
    "C3Y" => 'C',
    "C4R" => 'C',
    "C5C" => 'C',
    "C6C" => 'C',
    "CAF" => 'C',
    "CAS" => 'C',
    "CAY" => 'C',
    "CCL" => 'K',
    "CCS" => 'C',
    "CEA" => 'C',
    "CG6" => 'C',
    "CGA" => 'E',
    "CGU" => 'E',
    "CHP" => 'G',
    "CIR" => 'R',
    "CLE" => 'L',
    "CLG" => 'K',
    "CLH" => 'K',
    "CME" => 'C',
    "CMH" => 'C',
    "CML" => 'C',
    "CMT" => 'C',
    "CR5" => 'G',
    "CS0" => 'C',
    "CS1" => 'C',
    "CS3" => 'C',
    "CS4" => 'C',
    "CSA" => 'C',
    "CSB" => 'C',
    "CSD" => 'C',
    "CSE" => 'C',
    "CSJ" => 'C',
    "CSO" => 'C',
    "CSP" => 'C',
    "CSR" => 'C',
    "CSS" => 'C',
    "CSU" => 'C',
    "CSW" => 'C',
    "CSX" => 'C',
    "CSZ" => 'C',
    "CTE" => 'W',
    "CTH" => 'T',
    "CWR" => 'S',
    "CXM" => 'M',
    "CY0" => 'C',
    "CY1" => 'C',
    "CY3" => 'C',
    "CY4" => 'C',
    "CYA" => 'C',
    "CYD" => 'C',
    "CYF" => 'C',
    "CYG" => 'C',
    "CYJ" => 'K',
    "CYM" => 'C',
    "CYQ" => 'C',
    "CYR" => 'C',
    "CYS" => 'C',
    "CZ2" => 'C',
    "CZZ" => 'C',
    "D11" => 'T',
    "D3P" => 'G',
    "DAB" => 'A',
    "DAH" => 'F',
    "DAL" => 'A',
    "DAR" => 'R',
    "DAS" => 'D',
    "DBB" => 'T',
    "DBS" => 'S',
    "DBU" => 'T',
    "DBY" => 'Y',
    "DBZ" => 'A',
    "DC2" => 'C',
    "DCY" => 'C',
    "DDE" => 'H',
    "DGH" => 'G',
    "DGL" => 'E',
    "DGN" => 'Q',
    "DHA" => 'S',
    "DHI" => 'H',
    "DHN" => 'V',
    "DHV" => 'V',
    "DI7" => 'Y',
    "DIL" => 'I',
    "DIR" => 'R',
    "DIV" => 'V',
    "DLE" => 'L',
    "DLS" => 'K',
    "DLY" => 'K',
    "DM0" => 'K',
    "DMH" => 'N',
    "DMK" => 'D',
    "DNE" => 'L',
    "DNL" => 'K',
    "DNP" => 'A',
    "DNS" => 'K',
    "DOH" => 'D',
    "DON" => 'L',
    "DPL" => 'P',
    "DPN" => 'F',
    "DPP" => 'A',
    "DPQ" => 'Y',
    "DPR" => 'P',
    "DSE" => 'S',
    "DSG" => 'N',
    "DSN" => 'S',
    "DSP" => 'D',
    "DTH" => 'T',
    "DTR" => 'W',
    "DTY" => 'Y',
    "DVA" => 'V',
    "DYS" => 'C',
    "ECC" => 'Q',
    "EFC" => 'C',
    "EHP" => 'F',
    "ESB" => 'Y',
    "ESC" => 'M',
    "EXY" => 'L',
    "F2F" => 'F',
    "FAK" => 'K',
    "FB5" => 'A',
    "FB6" => 'A',
    "FCL" => 'F',
    "FGA" => 'E',
    "FGL" => 'G',
    "FGP" => 'S',
    "FH7" => 'K',
    "FHL" => 'K',
    "FHO" => 'K',
    "FLA" => 'A',
    "FLE" => 'L',
    "FLT" => 'Y',
    "FME" => 'M',
    "FOE" => 'C',
    "FP9" => 'P',
    "FT6" => 'W',
    "FTR" => 'W',
    "FTY" => 'Y',
    "FVA" => 'V',
    "FZN" => 'K',
    "GAU" => 'E',
    "GFT" => 'S',
    "GGL" => 'E',
    "GHG" => 'Q',
    "GHP" => 'G',
    "GL3" => 'G',
    "GLH" => 'Q',
    "GLJ" => 'E',
    "GLK" => 'E',
    "GLN" => 'Q',
    "GLQ" => 'E',
    "GLU" => 'E',
    "GLY" => 'G',
    "GLZ" => 'G',
    "GMA" => 'E',
    "GPL" => 'K',
    "GSC" => 'G',
    "GSU" => 'E',
    "GT9" => 'C',
    "GVL" => 'S',
    "H14" => 'F',
    "H5M" => 'P',
    "HAC" => 'A',
    "HAR" => 'R',
    "HBN" => 'H',
    "HHI" => 'H',
    "HIA" => 'H',
    "HIC" => 'H',
    "HIP" => 'H',
    "HIQ" => 'H',
    "HIS" => 'H',
    "HL2" => 'L',
    "HLU" => 'L',
    "HMR" => 'R',
    "HPC" => 'F',
    "HPE" => 'F',
    "HPH" => 'F',
    "HPQ" => 'F',
    "HQA" => 'A',
    "HRG" => 'R',
    "HRP" => 'W',
    "HS8" => 'H',
    "HS9" => 'H',
    "HSE" => 'S',
    "HSL" => 'S',
    "HSO" => 'H',
    "HSV" => 'H',
    "HTI" => 'C',
    "HTN" => 'N',
    "HTR" => 'W',
    "HV5" => 'A',
    "HVA" => 'V',
    "HY3" => 'P',
    "HYP" => 'P',
    "HZP" => 'P',
    "I2M" => 'I',
    "I58" => 'K',
    "IAM" => 'A',
    "IAR" => 'R',
    "IAS" => 'D',
    "IEL" => 'K',
    "IGL" => 'G',
    "IIL" => 'I',
    "ILE" => 'I',
    "ILG" => 'E',
    "ILX" => 'I',
    "IML" => 'I',
    "IOY" => 'F',
    "IPG" => 'G',
    "IT1" => 'K',
    "IYR" => 'Y',
    "IYT" => 'T',
    "IZO" => 'M',
    "JJJ" => 'C',
    "JJK" => 'C',
    "JJL" => 'C',
    "K1R" => 'C',
    "KCX" => 'K',
    "KGC" => 'K',
    "KNB" => 'A',
    "KOR" => 'M',
    "KPF" => 'K',
    "KPI" => 'K',
    "KST" => 'K',
    "KYN" => 'W',
    "KYQ" => 'K',
    "LA2" => 'K',
    "LAA" => 'D',
    "LAL" => 'A',
    "LBY" => 'K',
    "LCK" => 'K',
    "LCX" => 'K',
    "LDH" => 'K',
    "LED" => 'L',
    "LEF" => 'L',
    "LEH" => 'L',
    "LEI" => 'V',
    "LEM" => 'L',
    "LEN" => 'L',
    "LET" => 'K',
    "LEU" => 'L',
    "LEX" => 'L',
    "LLP" => 'K',
    "LLY" => 'K',
    "LME" => 'E',
    "LMF" => 'K',
    "LMQ" => 'Q',
    "LP6" => 'K',
    "LPD" => 'P',
    "LPG" => 'G',
    "LPS" => 'S',
    "LSO" => 'K',
    "LTR" => 'W',
    "LVG" => 'G',
    "LVN" => 'V',
    "LYF" => 'K',
    "LYK" => 'K',
    "LYM" => 'K',
    "LYN" => 'K',
    "LYR" => 'K',
    "LYS" => 'K',
    "LYX" => 'K',
    "LYZ" => 'K',
    "M0H" => 'C',
    "M2L" => 'K',
    "M2S" => 'M',
    "M30" => 'G',
    "M3L" => 'K',
    "MAA" => 'A',
    "MAI" => 'R',
    "MBQ" => 'Y',
    "MC1" => 'S',
    "MCL" => 'K',
    "MCS" => 'C',
    "MD3" => 'C',
    "MD6" => 'G',
    "MDF" => 'Y',
    "MEA" => 'F',
    "MED" => 'M',
    "MEG" => 'E',
    "MEN" => 'N',
    "MEQ" => 'Q',
    "MET" => 'M',
    "MEU" => 'G',
    "MGG" => 'R',
    "MGN" => 'Q',
    "MGY" => 'G',
    "MHL" => 'L',
    "MHO" => 'M',
    "MHS" => 'H',
    "MIS" => 'S',
    "MK8" => 'L',
    "ML3" => 'K',
    "MLE" => 'L',
    "MLL" => 'L',
    "MLY" => 'K',
    "MLZ" => 'K',
    "MME" => 'M',
    "MMO" => 'R',
    "MND" => 'N',
    "MNL" => 'L',
    "MNV" => 'V',
    "MP8" => 'P',
    "MPQ" => 'G',
    "MSA" => 'G',
    "MSE" => 'M',
    "MSL" => 'M',
    "MSO" => 'M',
    "MT2" => 'M',
    "MTY" => 'Y',
    "MVA" => 'V',
    "N10" => 'S',
    "N7P" => 'P',
    "N80" => 'P',
    "N8P" => 'P',
    "NA8" => 'A',
    "NAL" => 'A',
    "NAM" => 'A',
    "NB8" => 'N',
    "NBQ" => 'Y',
    "NC1" => 'S',
    "NCB" => 'A',
    "NDF" => 'F',
    "NEM" => 'H',
    "NEP" => 'H',
    "NFA" => 'F',
    "NHL" => 'E',
    "NIY" => 'Y',
    "NLE" => 'L',
    "NLN" => 'L',
    "NLO" => 'L',
    "NLP" => 'L',
    "NLQ" => 'Q',
    "NLW" => 'L',
    "NMC" => 'G',
    "NMM" => 'R',
    "NNH" => 'R',
    "NPH" => 'C',
    "NPI" => 'A',
    "NTR" => 'Y',
    "NTY" => 'Y',
    "NVA" => 'V',
    "NYS" => 'C',
    "NZH" => 'H',
    "OAR" => 'R',
    "OAS" => 'S',
    "OBS" => 'K',
    "OCS" => 'C',
    "OCY" => 'C',
    "OHI" => 'H',
    "OHS" => 'D',
    "OLT" => 'T',
    "OLZ" => 'S',
    "OMT" => 'M',
    "ONH" => 'A',
    "OPR" => 'R',
    "ORN" => 'A',
    "ORQ" => 'R',
    "OSE" => 'S',
    "OTH" => 'T',
    "OXX" => 'D',
    "P1L" => 'C',
    "P2Y" => 'P',
    "PAQ" => 'Y',
    "PAS" => 'D',
    "PAT" => 'W',
    "PAU" => 'A',
    "PBB" => 'C',
    "PBF" => 'F',
    "PCA" => 'E',
    "PCC" => 'P',
    "PCS" => 'F',
    "PEC" => 'C',
    "PF5" => 'F',
    "PFF" => 'F',
    "PG1" => 'S',
    "PG9" => 'G',
    "PGY" => 'G',
    "PH6" => 'P',
    "PHA" => 'F',
    "PHD" => 'D',
    "PHE" => 'F',
    "PHI" => 'F',
    "PHL" => 'F',
    "PHM" => 'F',
    "PLE" => 'L',
    "PM3" => 'F',
    "POM" => 'P',
    "PPN" => 'F',
    "PR3" => 'C',
    "PR9" => 'P',
    "PRO" => 'P',
    "PRS" => 'P',
    "PSA" => 'F',
    "PSH" => 'H',
    "PTH" => 'Y',
    "PTM" => 'Y',
    "PTR" => 'Y',
    "PVH" => 'H',
    "PYA" => 'A',
    "PYX" => 'C',
    "QCS" => 'C',
    "QMM" => 'Q',
    "QPA" => 'C',
    "QPH" => 'F',
    "R1A" => 'C',
    "R4K" => 'W',
    "RE0" => 'W',
    "RE3" => 'W',
    "RPI" => 'R',
    "RVX" => 'S',
    "RZ4" => 'S',
    "S1H" => 'S',
    "S2C" => 'C',
    "S2D" => 'A',
    "S2P" => 'A',
    "SAC" => 'S',
    "SAH" => 'C',
    "SAR" => 'G',
    "SBL" => 'S',
    "SCH" => 'C',
    "SCS" => 'C',
    "SCY" => 'C',
    "SDP" => 'S',
    "SE7" => 'A',
    "SEB" => 'S',
    "SEG" => 'A',
    "SEL" => 'S',
    "SEM" => 'S',
    "SEN" => 'S',
    "SEP" => 'S',
    "SER" => 'S',
    "SET" => 'S',
    "SGB" => 'S',
    "SHC" => 'C',
    "SHP" => 'G',
    "SHR" => 'K',
    "SIB" => 'C',
    "SLR" => 'P',
    "SLZ" => 'K',
    "SMC" => 'C',
    "SME" => 'M',
    "SMF" => 'F',
    "SNC" => 'C',
    "SNN" => 'N',
    "SOC" => 'C',
    "SOY" => 'S',
    "SRZ" => 'S',
    "STY" => 'Y',
    "SUN" => 'S',
    "SVA" => 'S',
    "SVV" => 'S',
    "SVW" => 'S',
    "SVX" => 'S',
    "SVY" => 'S',
    "SVZ" => 'S',
    "SYS" => 'C',
    "T11" => 'F',
    "TAV" => 'D',
    "TBG" => 'V',
    "TBM" => 'T',
    "TCQ" => 'Y',
    "TCR" => 'W',
    "TDD" => 'L',
    "TFQ" => 'F',
    "TH6" => 'T',
    "THC" => 'T',
    "THR" => 'T',
    "THZ" => 'R',
    "TIH" => 'A',
    "TMB" => 'T',
    "TMD" => 'T',
    "TNB" => 'C',
    "TNR" => 'S',
    "TOQ" => 'W',
    "TPL" => 'W',
    "TPO" => 'T',
    "TPQ" => 'Y',
    "TQI" => 'W',
    "TQQ" => 'W',
    "TRF" => 'W',
    "TRG" => 'K',
    "TRN" => 'W',
    "TRO" => 'W',
    "TRP" => 'W',
    "TRQ" => 'W',
    "TRW" => 'W',
    "TRX" => 'W',
    "TRY" => 'W',
    "TTQ" => 'W',
    "TTS" => 'Y',
    "TXY" => 'Y',
    "TY1" => 'Y',
    "TY2" => 'Y',
    "TY3" => 'Y',
    "TY5" => 'Y',
    "TYB" => 'Y',
    "TYI" => 'Y',
    "TYJ" => 'Y',
    "TYN" => 'Y',
    "TYO" => 'Y',
    "TYQ" => 'Y',
    "TYR" => 'Y',
    "TYS" => 'Y',
    "TYT" => 'Y',
    "TYW" => 'Y',
    "TYY" => 'Y',
    "UMA" => 'A',
    "VAD" => 'V',
    "VAF" => 'V',
    "VAL" => 'V',
    "VB1" => 'K',
    "WLU" => 'L',
    "WPA" => 'F',
    "WRP" => 'W',
    "WVL" => 'V',
    "X2W" => 'E',
    "XCN" => 'C',
    "XDT" => 'T',
    "XPR" => 'P',
    "XSN" => 'N',
    "XX1" => 'K',
    "YCM" => 'C',
    "YOF" => 'Y',
    "YTH" => 'T',
    "Z01" => 'A',
    "ZAL" => 'A',
    "ZCL" => 'F',
    "ZU0" => 'T',
    "ZZJ" => 'A',
)