aa3Hash.put("VAL", new Integer(19));
// IUB Nomenclature for ambiguous peptides
aa3Hash.put("ASX", new Integer(20)); // "B";
- aa3Hash.put("GLX", new Integer(21)); // X
+ aa3Hash.put("GLX", new Integer(21)); // Z
aa3Hash.put("XAA", new Integer(22)); // X unknown
aa3Hash.put("-", new Integer(23));
aa3Hash.put("*", new Integer(23));
aa3Hash.put(".", new Integer(23));
aa3Hash.put(" ", new Integer(23));
aa3Hash.put("Gap", new Integer(23));
+ aa3Hash.put("UR3", new Integer(24));
}
static
public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E",
"G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B",
- "Z", "X", "_", "*", ".", " " };
+ "Z", "X", "_", "*", ".", " ", "U" };
public static final Color midBlue = new Color(100, 100, 255);
// modifications.put("5HP", "GLU"); // Pyroglutamic acid; 5-hydroxyproline
// modifications.put("PCA", "GLU"); // Pyroglutamic acid
// modifications.put("LYZ", "LYS"); // 5-hydroxylysine
+
+ // Additional protein alphabets used in the SCOP database and PDB files
+ // source:
+ // https://github.com/biopython/biopython/blob/master/Bio/Data/SCOPData.py
+ modifications.put("00C", "CYS");
+ modifications.put("01W", "XAA");
+ modifications.put("02K", "ALA");
+ modifications.put("03Y", "CYS");
+ modifications.put("07O", "CYS");
+ modifications.put("08P", "CYS");
+ modifications.put("0A0", "ASP");
+ modifications.put("0A1", "TYR");
+ modifications.put("0A2", "LYS");
+ modifications.put("0A8", "CYS");
+ modifications.put("0AA", "VAL");
+ modifications.put("0AB", "VAL");
+ modifications.put("0AC", "GLY");
+ modifications.put("0AD", "GLY");
+ modifications.put("0AF", "TRP");
+ modifications.put("0AG", "LEU");
+ modifications.put("0AH", "SER");
+ modifications.put("0AK", "ASP");
+ modifications.put("0AM", "ALA");
+ modifications.put("0AP", "CYS");
+ modifications.put("0AU", "UR3");
+ modifications.put("0AV", "ALA");
+ modifications.put("0AZ", "PRO");
+ modifications.put("0BN", "PHE");
+ modifications.put("0C ", "CYS");
+ modifications.put("0CS", "ALA");
+ modifications.put("0DC", "CYS");
+ modifications.put("0DG", "GLY");
+ modifications.put("0DT", "THR");
+ modifications.put("0FL", "ALA");
+ modifications.put("0G ", "GLY");
+ modifications.put("0NC", "ALA");
+ modifications.put("0SP", "ALA");
+ modifications.put("0U ", "UR3");
+ modifications.put("0YG", "YG");
+ modifications.put("10C", "CYS");
+ modifications.put("125", "UR3");
+ modifications.put("126", "UR3");
+ modifications.put("127", "UR3");
+ modifications.put("128", "ASN");
+ modifications.put("12A", "ALA");
+ modifications.put("143", "CYS");
+ modifications.put("175", "ASG");
+ modifications.put("193", "XAA");
+ modifications.put("1AP", "ALA");
+ modifications.put("1MA", "ALA");
+ modifications.put("1MG", "GLY");
+ modifications.put("1PA", "PHE");
+ modifications.put("1PI", "ALA");
+ modifications.put("1PR", "ASN");
+ modifications.put("1SC", "CYS");
+ modifications.put("1TQ", "TRP");
+ modifications.put("1TY", "TYR");
+ modifications.put("1X6", "SER");
+ modifications.put("200", "PHE");
+ modifications.put("23F", "PHE");
+ modifications.put("23S", "XAA");
+ modifications.put("26B", "THR");
+ modifications.put("2AD", "XAA");
+ modifications.put("2AG", "ALA");
+ modifications.put("2AO", "XAA");
+ modifications.put("2AR", "ALA");
+ modifications.put("2AS", "XAA");
+ modifications.put("2AT", "THR");
+ modifications.put("2AU", "UR3");
+ modifications.put("2BD", "ILE");
+ modifications.put("2BT", "THR");
+ modifications.put("2BU", "ALA");
+ modifications.put("2CO", "CYS");
+ modifications.put("2DA", "ALA");
+ modifications.put("2DF", "ASN");
+ modifications.put("2DM", "ASN");
+ modifications.put("2DO", "XAA");
+ modifications.put("2DT", "THR");
+ modifications.put("2EG", "GLY");
+ modifications.put("2FE", "ASN");
+ modifications.put("2FI", "ASN");
+ modifications.put("2FM", "MET");
+ modifications.put("2GT", "THR");
+ modifications.put("2HF", "HIS");
+ modifications.put("2LU", "LEU");
+ modifications.put("2MA", "ALA");
+ modifications.put("2MG", "GLY");
+ modifications.put("2ML", "LEU");
+ modifications.put("2MR", "ARG");
+ modifications.put("2MT", "PRO");
+ modifications.put("2MU", "UR3");
+ modifications.put("2NT", "THR");
+ modifications.put("2OM", "UR3");
+ modifications.put("2OT", "THR");
+ modifications.put("2PI", "XAA");
+ modifications.put("2PR", "GLY");
+ modifications.put("2SA", "ASN");
+ modifications.put("2SI", "XAA");
+ modifications.put("2ST", "THR");
+ modifications.put("2TL", "THR");
+ modifications.put("2TY", "TYR");
+ modifications.put("2VA", "VAL");
+ modifications.put("2XA", "CYS");
+ modifications.put("32S", "XAA");
+ modifications.put("32T", "XAA");
+ modifications.put("3AH", "HIS");
+ modifications.put("3AR", "XAA");
+ modifications.put("3CF", "PHE");
+ modifications.put("3DA", "ALA");
+ modifications.put("3DR", "ASN");
+ modifications.put("3GA", "ALA");
+ modifications.put("3MD", "ASP");
+ modifications.put("3ME", "UR3");
+ modifications.put("3NF", "TYR");
+ modifications.put("3QN", "LYS");
+ modifications.put("3TY", "XAA");
+ modifications.put("3XH", "GLY");
+ modifications.put("4AC", "ASN");
+ modifications.put("4BF", "TYR");
+ modifications.put("4CF", "PHE");
+ modifications.put("4CY", "MET");
+ modifications.put("4DP", "TRP");
+ modifications.put("4F3", "GYG");
+ modifications.put("4FB", "PRO");
+ modifications.put("4FW", "TRP");
+ modifications.put("4HT", "TRP");
+ modifications.put("4IN", "TRP");
+ modifications.put("4MF", "ASN");
+ modifications.put("4MM", "XAA");
+ modifications.put("4OC", "CYS");
+ modifications.put("4PC", "CYS");
+ modifications.put("4PD", "CYS");
+ modifications.put("4PE", "CYS");
+ modifications.put("4PH", "PHE");
+ modifications.put("4SC", "CYS");
+ modifications.put("4SU", "UR3");
+ modifications.put("4TA", "ASN");
+ modifications.put("4U7", "ALA");
+ modifications.put("56A", "HIS");
+ modifications.put("5AA", "ALA");
+ modifications.put("5AB", "ALA");
+ modifications.put("5AT", "THR");
+ modifications.put("5BU", "UR3");
+ modifications.put("5CG", "GLY");
+ modifications.put("5CM", "CYS");
+ modifications.put("5CS", "CYS");
+ modifications.put("5FA", "ALA");
+ modifications.put("5FC", "CYS");
+ modifications.put("5FU", "UR3");
+ modifications.put("5HP", "GLU");
+ modifications.put("5HT", "THR");
+ modifications.put("5HU", "UR3");
+ modifications.put("5IC", "CYS");
+ modifications.put("5IT", "THR");
+ modifications.put("5IU", "UR3");
+ modifications.put("5MC", "CYS");
+ modifications.put("5MD", "ASN");
+ modifications.put("5MU", "UR3");
+ modifications.put("5NC", "CYS");
+ modifications.put("5PC", "CYS");
+ modifications.put("5PY", "THR");
+ modifications.put("5SE", "UR3");
+ modifications.put("5ZA", "TWG");
+ modifications.put("64T", "THR");
+ modifications.put("6CL", "LYS");
+ modifications.put("6CT", "THR");
+ modifications.put("6CW", "TRP");
+ modifications.put("6HA", "ALA");
+ modifications.put("6HC", "CYS");
+ modifications.put("6HG", "GLY");
+ modifications.put("6HN", "LYS");
+ modifications.put("6HT", "THR");
+ modifications.put("6IA", "ALA");
+ modifications.put("6MA", "ALA");
+ modifications.put("6MC", "ALA");
+ modifications.put("6MI", "ASN");
+ modifications.put("6MT", "ALA");
+ modifications.put("6MZ", "ASN");
+ modifications.put("6OG", "GLY");
+ modifications.put("70U", "UR3");
+ modifications.put("7DA", "ALA");
+ modifications.put("7GU", "GLY");
+ modifications.put("7JA", "ILE");
+ modifications.put("7MG", "GLY");
+ modifications.put("8AN", "ALA");
+ modifications.put("8FG", "GLY");
+ modifications.put("8MG", "GLY");
+ modifications.put("8OG", "GLY");
+ modifications.put("9NE", "GLU");
+ modifications.put("9NF", "PHE");
+ modifications.put("9NR", "ARG");
+ modifications.put("9NV", "VAL");
+ modifications.put("A ", "ALA");
+ modifications.put("A1P", "ASN");
+ modifications.put("A23", "ALA");
+ modifications.put("A2L", "ALA");
+ modifications.put("A2M", "ALA");
+ modifications.put("A34", "ALA");
+ modifications.put("A35", "ALA");
+ modifications.put("A38", "ALA");
+ modifications.put("A39", "ALA");
+ modifications.put("A3A", "ALA");
+ modifications.put("A3P", "ALA");
+ modifications.put("A40", "ALA");
+ modifications.put("A43", "ALA");
+ modifications.put("A44", "ALA");
+ modifications.put("A47", "ALA");
+ modifications.put("A5L", "ALA");
+ modifications.put("A5M", "CYS");
+ modifications.put("A5N", "ASN");
+ modifications.put("A5O", "ALA");
+ modifications.put("A66", "XAA");
+ modifications.put("AA3", "ALA");
+ modifications.put("AA4", "ALA");
+ modifications.put("AAR", "ARG");
+ modifications.put("AB7", "XAA");
+ modifications.put("ABA", "ALA");
+ modifications.put("ABR", "ALA");
+ modifications.put("ABS", "ALA");
+ modifications.put("ABT", "ASN");
+ modifications.put("ACB", "ASP");
+ modifications.put("ACL", "ARG");
+ modifications.put("AD2", "ALA");
+ modifications.put("ADD", "XAA");
+ modifications.put("ADX", "ASN");
+ modifications.put("AEA", "XAA");
+ modifications.put("AEI", "ASP");
+ modifications.put("AET", "ALA");
+ modifications.put("AFA", "ASN");
+ modifications.put("AFF", "ASN");
+ modifications.put("AFG", "GLY");
+ modifications.put("AGM", "ARG");
+ modifications.put("AGT", "CYS");
+ modifications.put("AHB", "ASN");
+ modifications.put("AHH", "XAA");
+ modifications.put("AHO", "ALA");
+ modifications.put("AHP", "ALA");
+ modifications.put("AHS", "XAA");
+ modifications.put("AHT", "XAA");
+ modifications.put("AIB", "ALA");
+ modifications.put("AKL", "ASP");
+ modifications.put("AKZ", "ASP");
+ modifications.put("ALA", "ALA");
+ modifications.put("ALC", "ALA");
+ modifications.put("ALM", "ALA");
+ modifications.put("ALN", "ALA");
+ modifications.put("ALO", "THR");
+ modifications.put("ALQ", "XAA");
+ modifications.put("ALS", "ALA");
+ modifications.put("ALT", "ALA");
+ modifications.put("ALV", "ALA");
+ modifications.put("ALY", "LYS");
+ modifications.put("AN8", "ALA");
+ modifications.put("AP7", "ALA");
+ modifications.put("APE", "XAA");
+ modifications.put("APH", "ALA");
+ modifications.put("API", "LYS");
+ modifications.put("APK", "LYS");
+ modifications.put("APM", "XAA");
+ modifications.put("APP", "XAA");
+ modifications.put("AR2", "ARG");
+ modifications.put("AR4", "GLU");
+ modifications.put("AR7", "ARG");
+ modifications.put("ARG", "ARG");
+ modifications.put("ARM", "ARG");
+ modifications.put("ARO", "ARG");
+ modifications.put("ARV", "XAA");
+ modifications.put("AS ", "ALA");
+ modifications.put("AS2", "ASP");
+ modifications.put("AS9", "XAA");
+ modifications.put("ASA", "ASP");
+ modifications.put("ASB", "ASP");
+ modifications.put("ASI", "ASP");
+ modifications.put("ASK", "ASP");
+ modifications.put("ASL", "ASP");
+ modifications.put("ASM", "XAA");
+ modifications.put("ASN", "ASN");
+ modifications.put("ASP", "ASP");
+ modifications.put("ASQ", "ASP");
+ modifications.put("ASU", "ASN");
+ modifications.put("ASX", "ASX");
+ modifications.put("ATD", "THR");
+ modifications.put("ATL", "THR");
+ modifications.put("ATM", "THR");
+ modifications.put("AVC", "ALA");
+ modifications.put("AVN", "XAA");
+ modifications.put("AYA", "ALA");
+ modifications.put("AYG", "AYG");
+ modifications.put("AZK", "LYS");
+ modifications.put("AZS", "SER");
+ modifications.put("AZY", "TYR");
+ modifications.put("B1F", "PHE");
+ modifications.put("B1P", "ASN");
+ modifications.put("B2A", "ALA");
+ modifications.put("B2F", "PHE");
+ modifications.put("B2I", "ILE");
+ modifications.put("B2V", "VAL");
+ modifications.put("B3A", "ALA");
+ modifications.put("B3D", "ASP");
+ modifications.put("B3E", "GLU");
+ modifications.put("B3K", "LYS");
+ modifications.put("B3L", "XAA");
+ modifications.put("B3M", "XAA");
+ modifications.put("B3Q", "XAA");
+ modifications.put("B3S", "SER");
+ modifications.put("B3T", "XAA");
+ modifications.put("B3U", "HIS");
+ modifications.put("B3X", "ASN");
+ modifications.put("B3Y", "TYR");
+ modifications.put("BB6", "CYS");
+ modifications.put("BB7", "CYS");
+ modifications.put("BB8", "PHE");
+ modifications.put("BB9", "CYS");
+ modifications.put("BBC", "CYS");
+ modifications.put("BCS", "CYS");
+ modifications.put("BE2", "XAA");
+ modifications.put("BFD", "ASP");
+ modifications.put("BG1", "SER");
+ modifications.put("BGM", "GLY");
+ modifications.put("BH2", "ASP");
+ modifications.put("BHD", "ASP");
+ modifications.put("BIF", "PHE");
+ modifications.put("BIL", "XAA");
+ modifications.put("BIU", "ILE");
+ modifications.put("BJH", "XAA");
+ modifications.put("BLE", "LEU");
+ modifications.put("BLY", "LYS");
+ modifications.put("BMP", "ASN");
+ modifications.put("BMT", "THR");
+ modifications.put("BNN", "PHE");
+ modifications.put("BNO", "XAA");
+ modifications.put("BOE", "THR");
+ modifications.put("BOR", "ARG");
+ modifications.put("BPE", "CYS");
+ modifications.put("BRU", "UR3");
+ modifications.put("BSE", "SER");
+ modifications.put("BT5", "ASN");
+ modifications.put("BTA", "LEU");
+ modifications.put("BTC", "CYS");
+ modifications.put("BTR", "TRP");
+ modifications.put("BUC", "CYS");
+ modifications.put("BUG", "VAL");
+ modifications.put("BVP", "UR3");
+ modifications.put("BZG", "ASN");
+ modifications.put("C ", "CYS");
+ modifications.put("C12", "TYG");
+ modifications.put("C1X", "LYS");
+ modifications.put("C25", "CYS");
+ modifications.put("C2L", "CYS");
+ modifications.put("C2S", "CYS");
+ modifications.put("C31", "CYS");
+ modifications.put("C32", "CYS");
+ modifications.put("C34", "CYS");
+ modifications.put("C36", "CYS");
+ modifications.put("C37", "CYS");
+ modifications.put("C38", "CYS");
+ modifications.put("C3Y", "CYS");
+ modifications.put("C42", "CYS");
+ modifications.put("C43", "CYS");
+ modifications.put("C45", "CYS");
+ modifications.put("C46", "CYS");
+ modifications.put("C49", "CYS");
+ modifications.put("C4R", "CYS");
+ modifications.put("C4S", "CYS");
+ modifications.put("C5C", "CYS");
+ modifications.put("C66", "XAA");
+ modifications.put("C6C", "CYS");
+ modifications.put("C99", "TFG");
+ modifications.put("CAF", "CYS");
+ modifications.put("CAL", "XAA");
+ modifications.put("CAR", "CYS");
+ modifications.put("CAS", "CYS");
+ modifications.put("CAV", "XAA");
+ modifications.put("CAY", "CYS");
+ modifications.put("CB2", "CYS");
+ modifications.put("CBR", "CYS");
+ modifications.put("CBV", "CYS");
+ modifications.put("CCC", "CYS");
+ modifications.put("CCL", "LYS");
+ modifications.put("CCS", "CYS");
+ modifications.put("CCY", "CYG");
+ modifications.put("CDE", "XAA");
+ modifications.put("CDV", "XAA");
+ modifications.put("CDW", "CYS");
+ modifications.put("CEA", "CYS");
+ modifications.put("CFL", "CYS");
+ modifications.put("CFY", "FCYG"); // check
+ modifications.put("CG1", "GLY");
+ modifications.put("CGA", "GLU");
+ modifications.put("CGU", "GLU");
+ modifications.put("CH ", "CYS");
+ modifications.put("CH6", "MYG");
+ modifications.put("CH7", "KYG");
+ modifications.put("CHF", "XAA");
+ modifications.put("CHG", "XAA");
+ modifications.put("CHP", "GLY");
+ modifications.put("CHS", "XAA");
+ modifications.put("CIR", "ARG");
+ modifications.put("CJO", "GYG");
+ modifications.put("CLE", "LEU");
+ modifications.put("CLG", "LYS");
+ modifications.put("CLH", "LYS");
+ modifications.put("CLV", "AFG");
+ modifications.put("CM0", "ASN");
+ modifications.put("CME", "CYS");
+ modifications.put("CMH", "CYS");
+ modifications.put("CML", "CYS");
+ modifications.put("CMR", "CYS");
+ modifications.put("CMT", "CYS");
+ modifications.put("CNU", "UR3");
+ modifications.put("CP1", "CYS");
+ modifications.put("CPC", "XAA");
+ modifications.put("CPI", "XAA");
+ modifications.put("CQR", "GYG");
+ modifications.put("CR0", "TLG");
+ modifications.put("CR2", "GYG");
+ modifications.put("CR5", "GLY");
+ modifications.put("CR7", "KYG");
+ modifications.put("CR8", "HYG");
+ modifications.put("CRF", "TWG");
+ modifications.put("CRG", "THG");
+ modifications.put("CRK", "MYG");
+ modifications.put("CRO", "GYG");
+ modifications.put("CRQ", "QYG");
+ modifications.put("CRU", "EYG");
+ modifications.put("CRW", "ASG");
+ modifications.put("CRX", "ASG");
+ modifications.put("CS0", "CYS");
+ modifications.put("CS1", "CYS");
+ modifications.put("CS3", "CYS");
+ modifications.put("CS4", "CYS");
+ modifications.put("CS8", "ASN");
+ modifications.put("CSA", "CYS");
+ modifications.put("CSB", "CYS");
+ modifications.put("CSD", "CYS");
+ modifications.put("CSE", "CYS");
+ modifications.put("CSF", "CYS");
+ modifications.put("CSH", "SHG");
+ modifications.put("CSI", "GLY");
+ modifications.put("CSJ", "CYS");
+ modifications.put("CSL", "CYS");
+ modifications.put("CSO", "CYS");
+ modifications.put("CSP", "CYS");
+ modifications.put("CSR", "CYS");
+ modifications.put("CSS", "CYS");
+ modifications.put("CSU", "CYS");
+ modifications.put("CSW", "CYS");
+ modifications.put("CSX", "CYS");
+ modifications.put("CSY", "SYG");
+ modifications.put("CSZ", "CYS");
+ modifications.put("CTE", "TRP");
+ modifications.put("CTG", "THR");
+ modifications.put("CTH", "THR");
+ modifications.put("CUC", "XAA");
+ modifications.put("CWR", "SER");
+ modifications.put("CXM", "MET");
+ modifications.put("CY0", "CYS");
+ modifications.put("CY1", "CYS");
+ modifications.put("CY3", "CYS");
+ modifications.put("CY4", "CYS");
+ modifications.put("CYA", "CYS");
+ modifications.put("CYD", "CYS");
+ modifications.put("CYF", "CYS");
+ modifications.put("CYG", "CYS");
+ modifications.put("CYJ", "XAA");
+ modifications.put("CYM", "CYS");
+ modifications.put("CYQ", "CYS");
+ modifications.put("CYR", "CYS");
+ modifications.put("CYS", "CYS");
+ modifications.put("CZ2", "CYS");
+ modifications.put("CZO", "GYG");
+ modifications.put("CZZ", "CYS");
+ modifications.put("D11", "THR");
+ modifications.put("D1P", "ASN");
+ modifications.put("D3 ", "ASN");
+ modifications.put("D33", "ASN");
+ modifications.put("D3P", "GLY");
+ modifications.put("D3T", "THR");
+ modifications.put("D4M", "THR");
+ modifications.put("D4P", "XAA");
+ modifications.put("DA ", "ALA");
+ modifications.put("DA2", "XAA");
+ modifications.put("DAB", "ALA");
+ modifications.put("DAH", "PHE");
+ modifications.put("DAL", "ALA");
+ modifications.put("DAR", "ARG");
+ modifications.put("DAS", "ASP");
+ modifications.put("DBB", "THR");
+ modifications.put("DBM", "ASN");
+ modifications.put("DBS", "SER");
+ modifications.put("DBU", "THR");
+ modifications.put("DBY", "TYR");
+ modifications.put("DBZ", "ALA");
+ modifications.put("DC ", "CYS");
+ modifications.put("DC2", "CYS");
+ modifications.put("DCG", "GLY");
+ modifications.put("DCI", "XAA");
+ modifications.put("DCL", "XAA");
+ modifications.put("DCT", "CYS");
+ modifications.put("DCY", "CYS");
+ modifications.put("DDE", "HIS");
+ modifications.put("DDG", "GLY");
+ modifications.put("DDN", "UR3");
+ modifications.put("DDX", "ASN");
+ modifications.put("DFC", "CYS");
+ modifications.put("DFG", "GLY");
+ modifications.put("DFI", "XAA");
+ modifications.put("DFO", "XAA");
+ modifications.put("DFT", "ASN");
+ modifications.put("DG ", "GLY");
+ modifications.put("DGH", "GLY");
+ modifications.put("DGI", "GLY");
+ modifications.put("DGL", "GLU");
+ modifications.put("DGN", "GLN");
+ modifications.put("DHA", "SER");
+ modifications.put("DHI", "HIS");
+ modifications.put("DHL", "XAA");
+ modifications.put("DHN", "VAL");
+ modifications.put("DHP", "XAA");
+ modifications.put("DHU", "UR3");
+ modifications.put("DHV", "VAL");
+ modifications.put("DI ", "ILE");
+ modifications.put("DIL", "ILE");
+ modifications.put("DIR", "ARG");
+ modifications.put("DIV", "VAL");
+ modifications.put("DLE", "LEU");
+ modifications.put("DLS", "LYS");
+ modifications.put("DLY", "LYS");
+ modifications.put("DM0", "LYS");
+ modifications.put("DMH", "ASN");
+ modifications.put("DMK", "ASP");
+ modifications.put("DMT", "XAA");
+ modifications.put("DN ", "ASN");
+ modifications.put("DNE", "LEU");
+ modifications.put("DNG", "LEU");
+ modifications.put("DNL", "LYS");
+ modifications.put("DNM", "LEU");
+ modifications.put("DNP", "ALA");
+ modifications.put("DNR", "CYS");
+ modifications.put("DNS", "LYS");
+ modifications.put("DOA", "XAA");
+ modifications.put("DOC", "CYS");
+ modifications.put("DOH", "ASP");
+ modifications.put("DON", "LEU");
+ modifications.put("DPB", "THR");
+ modifications.put("DPH", "PHE");
+ modifications.put("DPL", "PRO");
+ modifications.put("DPP", "ALA");
+ modifications.put("DPQ", "TYR");
+ modifications.put("DPR", "PRO");
+ modifications.put("DPY", "ASN");
+ modifications.put("DRM", "UR3");
+ modifications.put("DRP", "ASN");
+ modifications.put("DRT", "THR");
+ modifications.put("DRZ", "ASN");
+ modifications.put("DSE", "SER");
+ modifications.put("DSG", "ASN");
+ modifications.put("DSN", "SER");
+ modifications.put("DSP", "ASP");
+ modifications.put("DT ", "THR");
+ modifications.put("DTH", "THR");
+ modifications.put("DTR", "TRP");
+ modifications.put("DTY", "TYR");
+ modifications.put("DU ", "UR3");
+ modifications.put("DVA", "VAL");
+ modifications.put("DXD", "ASN");
+ modifications.put("DXN", "ASN");
+ modifications.put("DYG", "DYG");
+ modifications.put("DYS", "CYS");
+ modifications.put("DZM", "ALA");
+ modifications.put("E ", "ALA");
+ modifications.put("E1X", "ALA");
+ modifications.put("ECC", "GLN");
+ modifications.put("EDA", "ALA");
+ modifications.put("EFC", "CYS");
+ modifications.put("EHP", "PHE");
+ modifications.put("EIT", "THR");
+ modifications.put("ENP", "ASN");
+ modifications.put("ESB", "TYR");
+ modifications.put("ESC", "MET");
+ modifications.put("EXB", "XAA");
+ modifications.put("EXY", "LEU");
+ modifications.put("EY5", "ASN");
+ modifications.put("EYS", "XAA");
+ modifications.put("F2F", "PHE");
+ modifications.put("FA2", "ALA");
+ modifications.put("FA5", "ASN");
+ modifications.put("FAG", "ASN");
+ modifications.put("FAI", "ASN");
+ modifications.put("FB5", "ALA");
+ modifications.put("FB6", "ALA");
+ modifications.put("FCL", "PHE");
+ modifications.put("FFD", "ASN");
+ modifications.put("FGA", "GLU");
+ modifications.put("FGL", "GLY");
+ modifications.put("FGP", "SER");
+ modifications.put("FHL", "XAA");
+ modifications.put("FHO", "LYS");
+ modifications.put("FHU", "UR3");
+ modifications.put("FLA", "ALA");
+ modifications.put("FLE", "LEU");
+ modifications.put("FLT", "TYR");
+ modifications.put("FME", "MET");
+ modifications.put("FMG", "GLY");
+ modifications.put("FMU", "ASN");
+ modifications.put("FOE", "CYS");
+ modifications.put("FOX", "GLY");
+ modifications.put("FP9", "PRO");
+ modifications.put("FPA", "PHE");
+ modifications.put("FRD", "XAA");
+ modifications.put("FT6", "TRP");
+ modifications.put("FTR", "TRP");
+ modifications.put("FTY", "TYR");
+ modifications.put("FVA", "VAL");
+ modifications.put("FZN", "LYS");
+ modifications.put("G ", "GLY");
+ modifications.put("G25", "GLY");
+ modifications.put("G2L", "GLY");
+ modifications.put("G2S", "GLY");
+ modifications.put("G31", "GLY");
+ modifications.put("G32", "GLY");
+ modifications.put("G33", "GLY");
+ modifications.put("G36", "GLY");
+ modifications.put("G38", "GLY");
+ modifications.put("G42", "GLY");
+ modifications.put("G46", "GLY");
+ modifications.put("G47", "GLY");
+ modifications.put("G48", "GLY");
+ modifications.put("G49", "GLY");
+ modifications.put("G4P", "ASN");
+ modifications.put("G7M", "GLY");
+ modifications.put("GAO", "GLY");
+ modifications.put("GAU", "GLU");
+ modifications.put("GCK", "CYS");
+ modifications.put("GCM", "XAA");
+ modifications.put("GDP", "GLY");
+ modifications.put("GDR", "GLY");
+ modifications.put("GFL", "GLY");
+ modifications.put("GGL", "GLU");
+ modifications.put("GH3", "GLY");
+ modifications.put("GHG", "GLN");
+ modifications.put("GHP", "GLY");
+ modifications.put("GL3", "GLY");
+ modifications.put("GLH", "GLN");
+ modifications.put("GLJ", "GLU");
+ modifications.put("GLK", "GLU");
+ modifications.put("GLM", "XAA");
+ modifications.put("GLN", "GLN");
+ modifications.put("GLQ", "GLU");
+ modifications.put("GLU", "GLU");
+ modifications.put("GLX", "GLX");
+ modifications.put("GLY", "GLY");
+ modifications.put("GLZ", "GLY");
+ modifications.put("GMA", "GLU");
+ modifications.put("GMS", "GLY");
+ modifications.put("GMU", "UR3");
+ modifications.put("GN7", "GLY");
+ modifications.put("GND", "XAA");
+ modifications.put("GNE", "ASN");
+ modifications.put("GOM", "GLY");
+ modifications.put("GPL", "LYS");
+ modifications.put("GS ", "GLY");
+ modifications.put("GSC", "GLY");
+ modifications.put("GSR", "GLY");
+ modifications.put("GSS", "GLY");
+ modifications.put("GSU", "GLU");
+ modifications.put("GT9", "CYS");
+ modifications.put("GTP", "GLY");
+ modifications.put("GVL", "XAA");
+ modifications.put("GYC", "CYG");
+ modifications.put("GYS", "SYG");
+ modifications.put("H2U", "UR3");
+ modifications.put("H5M", "PRO");
+ modifications.put("HAC", "ALA");
+ modifications.put("HAR", "ARG");
+ modifications.put("HBN", "HIS");
+ modifications.put("HCS", "XAA");
+ modifications.put("HDP", "UR3");
+ modifications.put("HEU", "UR3");
+ modifications.put("HFA", "XAA");
+ modifications.put("HGL", "XAA");
+ modifications.put("HHI", "HIS");
+ modifications.put("HHK", "AK"); // check
+ modifications.put("HIA", "HIS");
+ modifications.put("HIC", "HIS");
+ modifications.put("HIP", "HIS");
+ modifications.put("HIQ", "HIS");
+ modifications.put("HIS", "HIS");
+ modifications.put("HL2", "LEU");
+ modifications.put("HLU", "LEU");
+ modifications.put("HMR", "ARG");
+ modifications.put("HOL", "ASN");
+ modifications.put("HPC", "PHE");
+ modifications.put("HPE", "PHE");
+ modifications.put("HPH", "PHE");
+ modifications.put("HPQ", "PHE");
+ modifications.put("HQA", "ALA");
+ modifications.put("HRG", "ARG");
+ modifications.put("HRP", "TRP");
+ modifications.put("HS8", "HIS");
+ modifications.put("HS9", "HIS");
+ modifications.put("HSE", "SER");
+ modifications.put("HSL", "SER");
+ modifications.put("HSO", "HIS");
+ modifications.put("HTI", "CYS");
+ modifications.put("HTN", "ASN");
+ modifications.put("HTR", "TRP");
+ modifications.put("HV5", "ALA");
+ modifications.put("HVA", "VAL");
+ modifications.put("HY3", "PRO");
+ modifications.put("HYP", "PRO");
+ modifications.put("HZP", "PRO");
+ modifications.put("I ", "ILE");
+ modifications.put("I2M", "ILE");
+ modifications.put("I58", "LYS");
+ modifications.put("I5C", "CYS");
+ modifications.put("IAM", "ALA");
+ modifications.put("IAR", "ARG");
+ modifications.put("IAS", "ASP");
+ modifications.put("IC ", "CYS");
+ modifications.put("IEL", "LYS");
+ modifications.put("IEY", "HYG");
+ modifications.put("IG ", "GLY");
+ modifications.put("IGL", "GLY");
+ modifications.put("IGU", "GLY");
+ modifications.put("IIC", "SHG");
+ modifications.put("IIL", "ILE");
+ modifications.put("ILE", "ILE");
+ modifications.put("ILG", "GLU");
+ modifications.put("ILX", "ILE");
+ modifications.put("IMC", "CYS");
+ modifications.put("IML", "ILE");
+ modifications.put("IOY", "PHE");
+ modifications.put("IPG", "GLY");
+ modifications.put("IPN", "ASN");
+ modifications.put("IRN", "ASN");
+ modifications.put("IT1", "LYS");
+ modifications.put("IU ", "UR3");
+ modifications.put("IYR", "TYR");
+ modifications.put("IYT", "THR");
+ modifications.put("IZO", "MET");
+ modifications.put("JJJ", "CYS");
+ modifications.put("JJK", "CYS");
+ modifications.put("JJL", "CYS");
+ modifications.put("JW5", "ASN");
+ modifications.put("K1R", "CYS");
+ modifications.put("KAG", "GLY");
+ modifications.put("KCX", "LYS");
+ modifications.put("KGC", "LYS");
+ modifications.put("KNB", "ALA");
+ modifications.put("KOR", "MET");
+ modifications.put("KPI", "LYS");
+ modifications.put("KST", "LYS");
+ modifications.put("KYQ", "LYS");
+ modifications.put("L2A", "XAA");
+ modifications.put("LA2", "LYS");
+ modifications.put("LAA", "ASP");
+ modifications.put("LAL", "ALA");
+ modifications.put("LBY", "LYS");
+ modifications.put("LC ", "CYS");
+ modifications.put("LCA", "ALA");
+ modifications.put("LCC", "ASN");
+ modifications.put("LCG", "GLY");
+ modifications.put("LCH", "ASN");
+ modifications.put("LCK", "LYS");
+ modifications.put("LCX", "LYS");
+ modifications.put("LDH", "LYS");
+ modifications.put("LED", "LEU");
+ modifications.put("LEF", "LEU");
+ modifications.put("LEH", "LEU");
+ modifications.put("LEI", "VAL");
+ modifications.put("LEM", "LEU");
+ modifications.put("LEN", "LEU");
+ modifications.put("LET", "XAA");
+ modifications.put("LEU", "LEU");
+ modifications.put("LEX", "LEU");
+ modifications.put("LG ", "GLY");
+ modifications.put("LGP", "GLY");
+ modifications.put("LHC", "XAA");
+ modifications.put("LHU", "UR3");
+ modifications.put("LKC", "ASN");
+ modifications.put("LLP", "LYS");
+ modifications.put("LLY", "LYS");
+ modifications.put("LME", "GLU");
+ modifications.put("LMF", "LYS");
+ modifications.put("LMQ", "GLN");
+ modifications.put("LMS", "ASN");
+ modifications.put("LP6", "LYS");
+ modifications.put("LPD", "PRO");
+ modifications.put("LPG", "GLY");
+ modifications.put("LPL", "XAA");
+ modifications.put("LPS", "SER");
+ modifications.put("LSO", "XAA");
+ modifications.put("LTA", "XAA");
+ modifications.put("LTR", "TRP");
+ modifications.put("LVG", "GLY");
+ modifications.put("LVN", "VAL");
+ modifications.put("LYF", "LYS");
+ modifications.put("LYK", "LYS");
+ modifications.put("LYM", "LYS");
+ modifications.put("LYN", "LYS");
+ modifications.put("LYR", "LYS");
+ modifications.put("LYS", "LYS");
+ modifications.put("LYX", "LYS");
+ modifications.put("LYZ", "LYS");
+ modifications.put("M0H", "CYS");
+ modifications.put("M1G", "GLY");
+ modifications.put("M2G", "GLY");
+ modifications.put("M2L", "LYS");
+ modifications.put("M2S", "MET");
+ modifications.put("M30", "GLY");
+ modifications.put("M3L", "LYS");
+ modifications.put("M5M", "CYS");
+ modifications.put("MA ", "ALA");
+ modifications.put("MA6", "ALA");
+ modifications.put("MA7", "ALA");
+ modifications.put("MAA", "ALA");
+ modifications.put("MAD", "ALA");
+ modifications.put("MAI", "ARG");
+ modifications.put("MBQ", "TYR");
+ modifications.put("MBZ", "ASN");
+ modifications.put("MC1", "SER");
+ modifications.put("MCG", "XAA");
+ modifications.put("MCL", "LYS");
+ modifications.put("MCS", "CYS");
+ modifications.put("MCY", "CYS");
+ modifications.put("MD3", "CYS");
+ modifications.put("MD6", "GLY");
+ modifications.put("MDH", "XAA");
+ modifications.put("MDO", "ASG");
+ modifications.put("MDR", "ASN");
+ modifications.put("MEA", "PHE");
+ modifications.put("MED", "MET");
+ modifications.put("MEG", "GLU");
+ modifications.put("MEN", "ASN");
+ modifications.put("MEP", "UR3");
+ modifications.put("MEQ", "GLN");
+ modifications.put("MET", "MET");
+ modifications.put("MEU", "GLY");
+ modifications.put("MF3", "XAA");
+ modifications.put("MFC", "GYG");
+ modifications.put("MG1", "GLY");
+ modifications.put("MGG", "ARG");
+ modifications.put("MGN", "GLN");
+ modifications.put("MGQ", "ALA");
+ modifications.put("MGV", "GLY");
+ modifications.put("MGY", "GLY");
+ modifications.put("MHL", "LEU");
+ modifications.put("MHO", "MET");
+ modifications.put("MHS", "HIS");
+ modifications.put("MIA", "ALA");
+ modifications.put("MIS", "SER");
+ modifications.put("MK8", "LEU");
+ modifications.put("ML3", "LYS");
+ modifications.put("MLE", "LEU");
+ modifications.put("MLL", "LEU");
+ modifications.put("MLY", "LYS");
+ modifications.put("MLZ", "LYS");
+ modifications.put("MME", "MET");
+ modifications.put("MMO", "ARG");
+ modifications.put("MMT", "THR");
+ modifications.put("MND", "ASN");
+ modifications.put("MNL", "LEU");
+ modifications.put("MNU", "UR3");
+ modifications.put("MNV", "VAL");
+ modifications.put("MOD", "XAA");
+ modifications.put("MP8", "PRO");
+ modifications.put("MPH", "XAA");
+ modifications.put("MPJ", "XAA");
+ modifications.put("MPQ", "GLY");
+ modifications.put("MRG", "GLY");
+ modifications.put("MSA", "GLY");
+ modifications.put("MSE", "MET");
+ modifications.put("MSL", "MET");
+ modifications.put("MSO", "MET");
+ modifications.put("MSP", "XAA");
+ modifications.put("MT2", "MET");
+ modifications.put("MTR", "THR");
+ modifications.put("MTU", "ALA");
+ modifications.put("MTY", "TYR");
+ modifications.put("MVA", "VAL");
+ modifications.put("N ", "ASN");
+ modifications.put("N10", "SER");
+ modifications.put("N2C", "XAA");
+ modifications.put("N5I", "ASN");
+ modifications.put("N5M", "CYS");
+ modifications.put("N6G", "GLY");
+ modifications.put("N7P", "PRO");
+ modifications.put("NA8", "ALA");
+ modifications.put("NAL", "ALA");
+ modifications.put("NAM", "ALA");
+ modifications.put("NB8", "ASN");
+ modifications.put("NBQ", "TYR");
+ modifications.put("NC1", "SER");
+ modifications.put("NCB", "ALA");
+ modifications.put("NCX", "ASN");
+ modifications.put("NCY", "XAA");
+ modifications.put("NDF", "PHE");
+ modifications.put("NDN", "UR3");
+ modifications.put("NEM", "HIS");
+ modifications.put("NEP", "HIS");
+ modifications.put("NF2", "ASN");
+ modifications.put("NFA", "PHE");
+ modifications.put("NHL", "GLU");
+ modifications.put("NIT", "XAA");
+ modifications.put("NIY", "TYR");
+ modifications.put("NLE", "LEU");
+ modifications.put("NLN", "LEU");
+ modifications.put("NLO", "LEU");
+ modifications.put("NLP", "LEU");
+ modifications.put("NLQ", "GLN");
+ modifications.put("NMC", "GLY");
+ modifications.put("NMM", "ARG");
+ modifications.put("NMS", "THR");
+ modifications.put("NMT", "THR");
+ modifications.put("NNH", "ARG");
+ modifications.put("NP3", "ASN");
+ modifications.put("NPH", "CYS");
+ modifications.put("NPI", "ALA");
+ modifications.put("NRP", "LYG");
+ modifications.put("NRQ", "MYG");
+ modifications.put("NSK", "XAA");
+ modifications.put("NTY", "TYR");
+ modifications.put("NVA", "VAL");
+ modifications.put("NYC", "TWG");
+ modifications.put("NYG", "NYG");
+ modifications.put("NYM", "ASN");
+ modifications.put("NYS", "CYS");
+ modifications.put("NZH", "HIS");
+ modifications.put("O12", "XAA");
+ modifications.put("O2C", "ASN");
+ modifications.put("O2G", "GLY");
+ modifications.put("OAD", "ASN");
+ modifications.put("OAS", "SER");
+ modifications.put("OBF", "XAA");
+ modifications.put("OBS", "XAA");
+ modifications.put("OCS", "CYS");
+ modifications.put("OCY", "CYS");
+ modifications.put("ODP", "ASN");
+ modifications.put("OHI", "HIS");
+ modifications.put("OHS", "ASP");
+ modifications.put("OIC", "XAA");
+ modifications.put("OIP", "ILE");
+ modifications.put("OLE", "XAA");
+ modifications.put("OLT", "THR");
+ modifications.put("OLZ", "SER");
+ modifications.put("OMC", "CYS");
+ modifications.put("OMG", "GLY");
+ modifications.put("OMT", "MET");
+ modifications.put("OMU", "UR3");
+ modifications.put("ONE", "UR3");
+ modifications.put("ONH", "ALA");
+ modifications.put("ONL", "XAA");
+ modifications.put("OPR", "ARG");
+ modifications.put("ORN", "ALA");
+ modifications.put("ORQ", "ARG");
+ modifications.put("OSE", "SER");
+ modifications.put("OTB", "XAA");
+ modifications.put("OTH", "THR");
+ modifications.put("OTY", "TYR");
+ modifications.put("OXX", "ASP");
+ modifications.put("P ", "GLY");
+ modifications.put("P1L", "CYS");
+ modifications.put("P1P", "ASN");
+ modifications.put("P2T", "THR");
+ modifications.put("P2U", "UR3");
+ modifications.put("P2Y", "PRO");
+ modifications.put("P5P", "ALA");
+ modifications.put("PAQ", "TYR");
+ modifications.put("PAS", "ASP");
+ modifications.put("PAT", "TRP");
+ modifications.put("PAU", "ALA");
+ modifications.put("PBB", "CYS");
+ modifications.put("PBF", "PHE");
+ modifications.put("PBT", "ASN");
+ modifications.put("PCA", "GLU");
+ modifications.put("PCC", "PRO");
+ modifications.put("PCE", "XAA");
+ modifications.put("PCS", "PHE");
+ modifications.put("PDL", "XAA");
+ modifications.put("PDU", "UR3");
+ modifications.put("PEC", "CYS");
+ modifications.put("PF5", "PHE");
+ modifications.put("PFF", "PHE");
+ modifications.put("PFX", "XAA");
+ modifications.put("PG1", "SER");
+ modifications.put("PG7", "GLY");
+ modifications.put("PG9", "GLY");
+ modifications.put("PGL", "XAA");
+ modifications.put("PGN", "GLY");
+ modifications.put("PGP", "GLY");
+ modifications.put("PGY", "GLY");
+ modifications.put("PHA", "PHE");
+ modifications.put("PHD", "ASP");
+ modifications.put("PHE", "PHE");
+ modifications.put("PHI", "PHE");
+ modifications.put("PHL", "PHE");
+ modifications.put("PHM", "PHE");
+ modifications.put("PIA", "AYG");
+ modifications.put("PIV", "XAA");
+ modifications.put("PLE", "LEU");
+ modifications.put("PM3", "PHE");
+ modifications.put("PMT", "CYS");
+ modifications.put("POM", "PRO");
+ modifications.put("PPN", "PHE");
+ modifications.put("PPU", "ALA");
+ modifications.put("PPW", "GLY");
+ modifications.put("PQ1", "ASN");
+ modifications.put("PR3", "CYS");
+ modifications.put("PR5", "ALA");
+ modifications.put("PR9", "PRO");
+ modifications.put("PRN", "ALA");
+ modifications.put("PRO", "PRO");
+ modifications.put("PRS", "PRO");
+ modifications.put("PSA", "PHE");
+ modifications.put("PSH", "HIS");
+ modifications.put("PST", "THR");
+ modifications.put("PSU", "UR3");
+ modifications.put("PSW", "CYS");
+ modifications.put("PTA", "XAA");
+ modifications.put("PTH", "TYR");
+ modifications.put("PTM", "TYR");
+ modifications.put("PTR", "TYR");
+ modifications.put("PU ", "ALA");
+ modifications.put("PUY", "ASN");
+ modifications.put("PVH", "HIS");
+ modifications.put("PVL", "XAA");
+ modifications.put("PYA", "ALA");
+ modifications.put("PYO", "UR3");
+ modifications.put("PYX", "CYS");
+ modifications.put("PYY", "ASN");
+ modifications.put("QLG", "QLG");
+ modifications.put("QMM", "GLN");
+ modifications.put("QPA", "CYS");
+ modifications.put("QPH", "PHE");
+ modifications.put("QUO", "GLY");
+ modifications.put("R ", "ALA");
+ modifications.put("R1A", "CYS");
+ modifications.put("R4K", "TRP");
+ modifications.put("RC7", "HYG");
+ modifications.put("RE0", "TRP");
+ modifications.put("RE3", "TRP");
+ modifications.put("RIA", "ALA");
+ modifications.put("RMP", "ALA");
+ modifications.put("RON", "XAA");
+ modifications.put("RT ", "THR");
+ modifications.put("RTP", "ASN");
+ modifications.put("S1H", "SER");
+ modifications.put("S2C", "CYS");
+ modifications.put("S2D", "ALA");
+ modifications.put("S2M", "THR");
+ modifications.put("S2P", "ALA");
+ modifications.put("S4A", "ALA");
+ modifications.put("S4C", "CYS");
+ modifications.put("S4G", "GLY");
+ modifications.put("S4U", "UR3");
+ modifications.put("S6G", "GLY");
+ modifications.put("SAC", "SER");
+ modifications.put("SAH", "CYS");
+ modifications.put("SAR", "GLY");
+ modifications.put("SBL", "SER");
+ modifications.put("SC ", "CYS");
+ modifications.put("SCH", "CYS");
+ modifications.put("SCS", "CYS");
+ modifications.put("SCY", "CYS");
+ modifications.put("SD2", "XAA");
+ modifications.put("SDG", "GLY");
+ modifications.put("SDP", "SER");
+ modifications.put("SEB", "SER");
+ modifications.put("SEC", "ALA");
+ modifications.put("SEG", "ALA");
+ modifications.put("SEL", "SER");
+ modifications.put("SEM", "SER");
+ modifications.put("SEN", "SER");
+ modifications.put("SEP", "SER");
+ modifications.put("SER", "SER");
+ modifications.put("SET", "SER");
+ modifications.put("SGB", "SER");
+ modifications.put("SHC", "CYS");
+ modifications.put("SHP", "GLY");
+ modifications.put("SHR", "LYS");
+ modifications.put("SIB", "CYS");
+ modifications.put("SIC", "DC"); // check
+ modifications.put("SLA", "PRO");
+ modifications.put("SLR", "PRO");
+ modifications.put("SLZ", "LYS");
+ modifications.put("SMC", "CYS");
+ modifications.put("SME", "MET");
+ modifications.put("SMF", "PHE");
+ modifications.put("SMP", "ALA");
+ modifications.put("SMT", "THR");
+ modifications.put("SNC", "CYS");
+ modifications.put("SNN", "ASN");
+ modifications.put("SOC", "CYS");
+ modifications.put("SOS", "ASN");
+ modifications.put("SOY", "SER");
+ modifications.put("SPT", "THR");
+ modifications.put("SRA", "ALA");
+ modifications.put("SSU", "UR3");
+ modifications.put("STY", "TYR");
+ modifications.put("SUB", "XAA");
+ modifications.put("SUI", "DG");
+ modifications.put("SUN", "SER");
+ modifications.put("SUR", "UR3");
+ modifications.put("SVA", "SER");
+ modifications.put("SVV", "SER");
+ modifications.put("SVW", "SER");
+ modifications.put("SVX", "SER");
+ modifications.put("SVY", "SER");
+ modifications.put("SVZ", "XAA");
+ modifications.put("SWG", "SWG");
+ modifications.put("SYS", "CYS");
+ modifications.put("T ", "THR");
+ modifications.put("T11", "PHE");
+ modifications.put("T23", "THR");
+ modifications.put("T2S", "THR");
+ modifications.put("T2T", "ASN");
+ modifications.put("T31", "UR3");
+ modifications.put("T32", "THR");
+ modifications.put("T36", "THR");
+ modifications.put("T37", "THR");
+ modifications.put("T38", "THR");
+ modifications.put("T39", "THR");
+ modifications.put("T3P", "THR");
+ modifications.put("T41", "THR");
+ modifications.put("T48", "THR");
+ modifications.put("T49", "THR");
+ modifications.put("T4S", "THR");
+ modifications.put("T5O", "UR3");
+ modifications.put("T5S", "THR");
+ modifications.put("T66", "XAA");
+ modifications.put("T6A", "ALA");
+ modifications.put("TA3", "THR");
+ modifications.put("TA4", "XAA");
+ modifications.put("TAF", "THR");
+ modifications.put("TAL", "ASN");
+ modifications.put("TAV", "ASP");
+ modifications.put("TBG", "VAL");
+ modifications.put("TBM", "THR");
+ modifications.put("TC1", "CYS");
+ modifications.put("TCP", "THR");
+ modifications.put("TCQ", "TYR");
+ modifications.put("TCR", "TRP");
+ modifications.put("TCY", "ALA");
+ modifications.put("TDD", "LEU");
+ modifications.put("TDY", "THR");
+ modifications.put("TFE", "THR");
+ modifications.put("TFO", "ALA");
+ modifications.put("TFQ", "PHE");
+ modifications.put("TFT", "THR");
+ modifications.put("TGP", "GLY");
+ modifications.put("TH6", "THR");
+ modifications.put("THC", "THR");
+ modifications.put("THO", "XAA");
+ modifications.put("THR", "THR");
+ modifications.put("THX", "ASN");
+ modifications.put("THZ", "ARG");
+ modifications.put("TIH", "ALA");
+ modifications.put("TLB", "ASN");
+ modifications.put("TLC", "THR");
+ modifications.put("TLN", "UR3");
+ modifications.put("TMB", "THR");
+ modifications.put("TMD", "THR");
+ modifications.put("TNB", "CYS");
+ modifications.put("TNR", "SER");
+ modifications.put("TOX", "TRP");
+ modifications.put("TP1", "THR");
+ modifications.put("TPC", "CYS");
+ modifications.put("TPG", "GLY");
+ modifications.put("TPH", "XAA");
+ modifications.put("TPL", "TRP");
+ modifications.put("TPO", "THR");
+ modifications.put("TPQ", "TYR");
+ modifications.put("TQI", "TRP");
+ modifications.put("TQQ", "TRP");
+ modifications.put("TRF", "TRP");
+ modifications.put("TRG", "LYS");
+ modifications.put("TRN", "TRP");
+ modifications.put("TRO", "TRP");
+ modifications.put("TRP", "TRP");
+ modifications.put("TRQ", "TRP");
+ modifications.put("TRW", "TRP");
+ modifications.put("TRX", "TRP");
+ modifications.put("TS ", "ASN");
+ modifications.put("TST", "XAA");
+ modifications.put("TT ", "ASN");
+ modifications.put("TTD", "THR");
+ modifications.put("TTI", "UR3");
+ modifications.put("TTM", "THR");
+ modifications.put("TTQ", "TRP");
+ modifications.put("TTS", "TYR");
+ modifications.put("TY1", "TYR");
+ modifications.put("TY2", "TYR");
+ modifications.put("TY3", "TYR");
+ modifications.put("TY5", "TYR");
+ modifications.put("TYB", "TYR");
+ modifications.put("TYI", "TYR");
+ modifications.put("TYJ", "TYR");
+ modifications.put("TYN", "TYR");
+ modifications.put("TYO", "TYR");
+ modifications.put("TYQ", "TYR");
+ modifications.put("TYR", "TYR");
+ modifications.put("TYS", "TYR");
+ modifications.put("TYT", "TYR");
+ modifications.put("TYU", "ASN");
+ modifications.put("TYW", "TYR");
+ modifications.put("TYX", "XAA");
+ modifications.put("TYY", "TYR");
+ modifications.put("TZB", "XAA");
+ modifications.put("TZO", "XAA");
+ modifications.put("U ", "UR3");
+ modifications.put("U25", "UR3");
+ modifications.put("U2L", "UR3");
+ modifications.put("U2N", "UR3");
+ modifications.put("U2P", "UR3");
+ modifications.put("U31", "UR3");
+ modifications.put("U33", "UR3");
+ modifications.put("U34", "UR3");
+ modifications.put("U36", "UR3");
+ modifications.put("U37", "UR3");
+ modifications.put("U8U", "UR3");
+ modifications.put("UAR", "UR3");
+ modifications.put("UCL", "UR3");
+ modifications.put("UD5", "UR3");
+ modifications.put("UDP", "ASN");
+ modifications.put("UFP", "ASN");
+ modifications.put("UFR", "UR3");
+ modifications.put("UFT", "UR3");
+ modifications.put("UMA", "ALA");
+ modifications.put("UMP", "UR3");
+ modifications.put("UMS", "UR3");
+ modifications.put("UN1", "XAA");
+ modifications.put("UN2", "XAA");
+ modifications.put("UNK", "XAA");
+ modifications.put("UR3", "UR3");
+ modifications.put("URD", "UR3");
+ modifications.put("US1", "UR3");
+ modifications.put("US2", "UR3");
+ modifications.put("US3", "THR");
+ modifications.put("US5", "UR3");
+ modifications.put("USM", "UR3");
+ modifications.put("VAD", "VAL");
+ modifications.put("VAF", "VAL");
+ modifications.put("VAL", "VAL");
+ modifications.put("VB1", "LYS");
+ modifications.put("VDL", "XAA");
+ modifications.put("VLL", "XAA");
+ modifications.put("VLM", "XAA");
+ modifications.put("VMS", "XAA");
+ modifications.put("VOL", "XAA");
+ modifications.put("WCR", "GYG");
+ modifications.put("X ", "GLY");
+ modifications.put("X2W", "GLU");
+ modifications.put("X4A", "ASN");
+ modifications.put("X9Q", "AFG");
+ modifications.put("XAD", "ALA");
+ modifications.put("XAE", "ASN");
+ modifications.put("XAL", "ALA");
+ modifications.put("XAR", "ASN");
+ modifications.put("XCL", "CYS");
+ modifications.put("XCN", "CYS");
+ modifications.put("XCP", "XAA");
+ modifications.put("XCR", "CYS");
+ modifications.put("XCS", "ASN");
+ modifications.put("XCT", "CYS");
+ modifications.put("XCY", "CYS");
+ modifications.put("XGA", "ASN");
+ modifications.put("XGL", "GLY");
+ modifications.put("XGR", "GLY");
+ modifications.put("XGU", "GLY");
+ modifications.put("XPR", "PRO");
+ modifications.put("XSN", "ASN");
+ modifications.put("XTH", "THR");
+ modifications.put("XTL", "THR");
+ modifications.put("XTR", "THR");
+ modifications.put("XTS", "GLY");
+ modifications.put("XTY", "ASN");
+ modifications.put("XUA", "ALA");
+ modifications.put("XUG", "GLY");
+ modifications.put("XX1", "LYS");
+ modifications.put("XXY", "THG");
+ modifications.put("XYG", "DYG");
+ modifications.put("Y ", "ALA");
+ modifications.put("YCM", "CYS");
+ modifications.put("YG ", "GLY");
+ modifications.put("YOF", "TYR");
+ modifications.put("YRR", "ASN");
+ modifications.put("YYG", "GLY");
+ modifications.put("Z ", "CYS");
+ modifications.put("Z01", "ALA");
+ modifications.put("ZAD", "ALA");
+ modifications.put("ZAL", "ALA");
+ modifications.put("ZBC", "CYS");
+ modifications.put("ZBU", "UR3");
+ modifications.put("ZCL", "PHE");
+ modifications.put("ZCY", "CYS");
+ modifications.put("ZDU", "UR3");
+ modifications.put("ZFB", "XAA");
+ modifications.put("ZGU", "GLY");
+ modifications.put("ZHP", "ASN");
+ modifications.put("ZTH", "THR");
+ modifications.put("ZU0", "THR");
+ modifications.put("ZZJ", "ALA");
+
}
public static String getCanonicalAminoAcid(String aa)
git://source.jalview.org / jalview.git / blobdiff