JAL-1479 JAL-1979 updated the modified-aminoacid triplet code dictionary in Jalview...

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index de99987..ad68b8a 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -245,13 +245,14 @@ public class ResidueProperties
     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
@@ -300,7 +301,7 @@ public class ResidueProperties
 
   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);
 
@@ -1695,6 +1696,1310 @@ public class ResidueProperties
     // 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)

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 7d5ae2e..9f7bc52 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -546,7 +546,8 @@ public class SiftsClient implements SiftsClientI
                   || seqCoordSys == CoordinateSys.UNIPROT)
           {
             char resCharCode = ResidueProperties
-                    .getSingleCharacterCode(residue.getDbResName());
+                    .getSingleCharacterCode(ResidueProperties
+                            .getCanonicalAminoAcid(residue.getDbResName()));
             resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
           }
           else

diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java
index 4dff315..b68ca68 100644 (file)
--- a/test/jalview/schemes/ResiduePropertiesTest.java
+++ b/test/jalview/schemes/ResiduePropertiesTest.java
@@ -242,6 +242,1307 @@ public class ResiduePropertiesTest
   {
     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
+
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("00C"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("01W"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("02K"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("03Y"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("07O"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("08P"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0A0"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("0A1"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("0A2"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0A8"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AA"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AB"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AD"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("0AF"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("0AG"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("0AH"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0AK"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0AP"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0AU"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AV"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("0AZ"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("0BN"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0C "));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0CS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0DC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0DG"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("0DT"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0FL"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0G "));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0NC"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0SP"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0U "));
+    assertEquals("YG", ResidueProperties.getCanonicalAminoAcid("0YG"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("10C"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("125"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("126"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("127"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("128"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("12A"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("143"));
+    assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("175"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("193"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1AP"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1MA"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("1MG"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("1PA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1PI"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("1PR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("1SC"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("1TQ"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("1TY"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("1X6"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("200"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("23F"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("23S"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("26B"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AD"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AG"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AO"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AR"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AS"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2AT"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2AU"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("2BD"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2BT"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2BU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2CO"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2DA"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DF"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DM"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2DO"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2DT"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2EG"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FE"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FI"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("2FM"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2GT"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("2HF"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2LU"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2MA"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2MG"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2ML"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("2MR"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("2MT"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2MU"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2NT"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2OM"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2OT"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2PI"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2PR"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2SA"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2SI"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2ST"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2TL"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("2TY"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("2VA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2XA"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32S"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32T"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("3AH"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3AR"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("3CF"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3DA"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("3DR"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3GA"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("3MD"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("3ME"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("3NF"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("3QN"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3TY"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("3XH"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4AC"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("4BF"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4CF"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("4CY"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4DP"));
+    assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("4F3"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("4FB"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4FW"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4HT"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4IN"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4MF"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("4MM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4OC"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PC"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PD"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PE"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4PH"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4SC"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("4SU"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4TA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("4U7"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("56A"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AB"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5AT"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5BU"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("5CG"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CS"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5FA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5FC"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5FU"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("5HP"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5HT"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5HU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5IC"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5IT"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5IU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5MC"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("5MD"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5MU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5NC"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5PC"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5PY"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5SE"));
+    assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("5ZA"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("64T"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6CL"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6CT"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("6CW"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6HA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("6HC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6HG"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6HN"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6HT"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6IA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MC"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MI"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MT"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MZ"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6OG"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("70U"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("7DA"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7GU"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("7JA"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7MG"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("8AN"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8FG"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8MG"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8OG"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("9NE"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("9NF"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("9NR"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("9NV"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A  "));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A1P"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A23"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2L"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2M"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A34"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A35"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A38"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A39"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3A"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3P"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A40"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A43"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A44"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A47"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5L"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("A5M"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A5N"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5O"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("A66"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA3"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA4"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AAR"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AB7"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABR"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABS"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ABT"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ACB"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ACL"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AD2"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ADD"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ADX"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AEA"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AEI"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AET"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFA"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFF"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("AFG"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AGM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("AGT"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AHB"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHH"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHO"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHP"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHT"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AIB"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKL"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKZ"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALC"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALM"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALN"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ALO"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ALQ"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALS"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALT"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALV"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ALY"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AN8"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AP7"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APE"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("APH"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("API"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("APK"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APM"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APP"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR2"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("AR4"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR7"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARG"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARM"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARO"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ARV"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AS "));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AS2"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AS9"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASA"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASB"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASI"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASK"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASL"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ASM"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASN"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASP"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASQ"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASU"));
+    assertEquals("ASX", ResidueProperties.getCanonicalAminoAcid("ASX"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATD"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATL"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATM"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AVC"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AVN"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AYA"));
+    assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("AYG"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("AZK"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("AZS"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("AZY"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B1F"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B1P"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B2A"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B2F"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("B2I"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("B2V"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B3A"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("B3D"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("B3E"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("B3K"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3L"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3M"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3Q"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("B3S"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3T"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("B3U"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B3X"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("B3Y"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB6"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB7"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BB8"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB9"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BBC"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BCS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BE2"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BFD"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BG1"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("BGM"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BH2"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BHD"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BIF"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BIL"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("BIU"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BJH"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BLE"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("BLY"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BMP"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BMT"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BNN"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BNO"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BOE"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("BOR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BPE"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BRU"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BSE"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BT5"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BTA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BTC"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("BTR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BUC"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("BUG"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BVP"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BZG"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C  "));
+    assertEquals("TYG", ResidueProperties.getCanonicalAminoAcid("C12"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("C1X"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C25"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2L"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2S"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C31"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C32"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C34"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C36"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C37"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C38"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C3Y"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C42"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C43"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C45"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C46"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C49"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4R"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4S"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C5C"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("C66"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C6C"));
+    assertEquals("TFG", ResidueProperties.getCanonicalAminoAcid("C99"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAF"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAV"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAY"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CB2"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBV"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCC"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CCL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCS"));
+    assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("CCY"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDE"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDV"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CDW"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CEA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CFL"));
+    assertEquals("FCYG", ResidueProperties.getCanonicalAminoAcid("CFY")); // check
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CG1"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGA"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CH "));
+    assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CH6"));
+    assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CH7"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHF"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHG"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CHP"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHS"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("CIR"));
+    assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CJO"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("CLE"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLG"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLH"));
+    assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("CLV"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CM0"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CME"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMH"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CML"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMT"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("CNU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CP1"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPC"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPI"));
+    assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CQR"));
+    assertEquals("TLG", ResidueProperties.getCanonicalAminoAcid("CR0"));
+    assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CR2"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CR5"));
+    assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CR7"));
+    assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("CR8"));
+    assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("CRF"));
+    assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("CRG"));
+    assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CRK"));
+    assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CRO"));
+    assertEquals("QYG", ResidueProperties.getCanonicalAminoAcid("CRQ"));
+    assertEquals("EYG", ResidueProperties.getCanonicalAminoAcid("CRU"));
+    assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRW"));
+    assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRX"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS0"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS1"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS3"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS4"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CS8"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSB"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSD"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSE"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSF"));
+    assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("CSH"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CSI"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSJ"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSO"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSP"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSW"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSX"));
+    assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("CSY"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSZ"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("CTE"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTG"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTH"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CUC"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("CWR"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("CXM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY0"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY1"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY3"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY4"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYD"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYF"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYG"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CYJ"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYQ"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZ2"));
+    assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CZO"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZZ"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D11"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D1P"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D3 "));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D33"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("D3P"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D3T"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D4M"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("D4P"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DA "));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DA2"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAB"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DAH"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAL"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DAR"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DAS"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBB"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DBM"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DBS"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBU"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DBY"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DBZ"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC "));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC2"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DCG"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCI"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCT"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCY"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DDE"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DDG"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DDN"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DDX"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DFC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DFG"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFI"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFO"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DFT"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DG "));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGH"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGI"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("DGL"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("DGN"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DHA"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DHI"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHL"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHN"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHP"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DHU"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHV"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DI "));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DIL"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DIR"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DIV"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DLE"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLS"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLY"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DM0"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DMH"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DMK"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DMT"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DN "));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNE"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNG"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNL"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNM"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DNP"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DNR"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DOA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DOC"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DOH"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DON"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DPB"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DPH"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPL"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DPP"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DPQ"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPR"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DPY"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DRM"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRP"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DRT"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRZ"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSE"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DSG"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSN"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DSP"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DT "));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DTH"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("DTR"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DTY"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DU "));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DVA"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXD"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXN"));
+    assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("DYG"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DYS"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DZM"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E  "));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E1X"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("ECC"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("EDA"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("EFC"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("EHP"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("EIT"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ENP"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("ESB"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("ESC"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EXB"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("EXY"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("EY5"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EYS"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("F2F"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FA2"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FA5"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAG"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAI"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB5"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB6"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FCL"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FFD"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("FGA"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FGL"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("FGP"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FHL"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FHO"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("FHU"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FLA"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("FLE"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FLT"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("FME"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FMG"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FMU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("FOE"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FOX"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("FP9"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FPA"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FRD"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FT6"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FTR"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FTY"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("FVA"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FZN"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G  "));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G25"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2L"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2S"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G31"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G32"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G33"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G36"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G38"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G42"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G46"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G47"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G48"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G49"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("G4P"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G7M"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GAO"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GAU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GCK"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GCM"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDP"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDR"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GFL"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GGL"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GH3"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GHG"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GHP"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GL3"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLH"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLJ"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLK"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GLM"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLN"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLQ"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLU"));
+    assertEquals("GLX", ResidueProperties.getCanonicalAminoAcid("GLX"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLY"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLZ"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GMA"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GMS"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("GMU"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GN7"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GND"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("GNE"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GOM"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("GPL"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GS "));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSR"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSS"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GSU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GT9"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GTP"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GVL"));
+    assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("GYC"));
+    assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("GYS"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("H2U"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("H5M"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HAC"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HAR"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HBN"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HCS"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HDP"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HEU"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HFA"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HGL"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HHI"));
+    assertEquals("AK", ResidueProperties.getCanonicalAminoAcid("HHK")); // check
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIA"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIC"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIP"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIQ"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIS"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HL2"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HLU"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HMR"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HOL"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPC"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPE"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPH"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPQ"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HQA"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HRG"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HRP"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS8"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS9"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSE"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSL"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HSO"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("HTI"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HTN"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HTR"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HV5"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("HVA"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HY3"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HYP"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HZP"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I  "));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I2M"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("I58"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("I5C"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("IAM"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("IAR"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("IAS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IC "));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IEL"));
+    assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("IEY"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IG "));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGL"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGU"));
+    assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("IIC"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IIL"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILE"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("ILG"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILX"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IMC"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IML"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("IOY"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IPG"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IPN"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IRN"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IT1"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("IU "));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("IYR"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("IYT"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("IZO"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJJ"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJK"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJL"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("JW5"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("K1R"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("KAG"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KCX"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KGC"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("KNB"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("KOR"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KPI"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KST"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KYQ"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("L2A"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LA2"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("LAA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LAL"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LBY"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("LC "));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LCA"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LCG"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCH"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCK"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCX"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LDH"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LED"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEF"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEH"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LEI"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEM"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEN"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LET"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEU"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEX"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LG "));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LGP"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LHC"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("LHU"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LKC"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLP"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLY"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("LME"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LMF"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("LMQ"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LMS"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LP6"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("LPD"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LPG"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LPL"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("LPS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LSO"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LTA"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("LTR"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LVG"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LVN"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYF"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYK"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYM"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYN"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYR"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYS"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYX"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYZ"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M0H"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M1G"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M2G"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M2L"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("M2S"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M30"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M3L"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M5M"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA "));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA6"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA7"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAD"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MAI"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MBQ"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MBZ"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MC1"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MCG"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MCL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCY"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MD3"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MD6"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MDH"));
+    assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("MDO"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MDR"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("MEA"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MED"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("MEG"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MEN"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MEP"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MEQ"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MEU"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MF3"));
+    assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("MFC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MG1"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MGG"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MGN"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MGQ"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGV"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGY"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MHL"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MHO"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("MHS"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MIA"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MIS"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MK8"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ML3"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLE"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLL"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLY"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLZ"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MME"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MMO"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MMT"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MND"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MNL"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MNU"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MNV"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MOD"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("MP8"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPH"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPJ"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MPQ"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MRG"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MSA"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSL"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSO"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MSP"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MT2"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MTR"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MTU"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MTY"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MVA"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N  "));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("N10"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("N2C"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N5I"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("N5M"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("N6G"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("N7P"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NA8"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAL"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAM"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NB8"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NBQ"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("NC1"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NCB"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NCX"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NCY"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NDF"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("NDN"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEM"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEP"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NF2"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NFA"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("NHL"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NIT"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NIY"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLE"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLN"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLO"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLP"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("NLQ"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("NMC"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NMM"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMS"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMT"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NNH"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NP3"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NPH"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NPI"));
+    assertEquals("LYG", ResidueProperties.getCanonicalAminoAcid("NRP"));
+    assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("NRQ"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NSK"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NTY"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("NVA"));
+    assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("NYC"));
+    assertEquals("NYG", ResidueProperties.getCanonicalAminoAcid("NYG"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NYM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NYS"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NZH"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("O12"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("O2C"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("O2G"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("OAD"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OAS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBF"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCY"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ODP"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("OHI"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OHS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OIC"));
+    assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("OIP"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OLE"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OLT"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OLZ"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OMC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("OMG"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("OMT"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("OMU"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ONE"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ONH"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ONL"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("OPR"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ORN"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ORQ"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OSE"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OTB"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OTH"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("OTY"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OXX"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("P  "));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("P1L"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("P1P"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("P2T"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("P2U"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("P2Y"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("P5P"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PAQ"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PAS"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("PAT"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PAU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PBB"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PBF"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PBT"));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("PCA"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PCC"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PCE"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PCS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PDL"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PDU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PEC"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PF5"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PFF"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PFX"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("PG1"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG7"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG9"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PGL"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGN"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGP"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGY"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHA"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PHD"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHE"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHI"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHL"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHM"));
+    assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("PIA"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PIV"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("PLE"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PM3"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PMT"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("POM"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PPN"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PPU"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PPW"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PQ1"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PR3"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PR5"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PR9"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PRN"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRO"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRS"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PSA"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PSH"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("PST"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PSU"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PSW"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PTA"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTH"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTM"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTR"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PU "));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PUY"));
+    assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PVH"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PVL"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PYA"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PYO"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PYX"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PYY"));
+    assertEquals("QLG", ResidueProperties.getCanonicalAminoAcid("QLG"));
+    assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("QMM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("QPA"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("QPH"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("QUO"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("R  "));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("R1A"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("R4K"));
+    assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("RC7"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE0"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE3"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RIA"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RMP"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("RON"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("RT "));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("RTP"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("S1H"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S2C"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2D"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("S2M"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2P"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S4A"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S4C"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S4G"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("S4U"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S6G"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SAC"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SAH"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SAR"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SBL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SC "));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCH"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCY"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SD2"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SDG"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SDP"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEB"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEC"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEG"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEL"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEM"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEN"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEP"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SER"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SET"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SGB"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SHC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SHP"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SHR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SIB"));
+    assertEquals("DC", ResidueProperties.getCanonicalAminoAcid("SIC")); // check
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLA"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLR"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SLZ"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SMC"));
+    assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("SME"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("SMF"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SMP"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SMT"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SNC"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SNN"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SOC"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SOS"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SOY"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SPT"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SRA"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SSU"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("STY"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SUB"));
+    assertEquals("DG", ResidueProperties.getCanonicalAminoAcid("SUI"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SUN"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SUR"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVA"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVV"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVW"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVX"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVY"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SVZ"));
+    assertEquals("SWG", ResidueProperties.getCanonicalAminoAcid("SWG"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SYS"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T  "));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("T11"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T23"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T2S"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("T2T"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T31"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T32"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T36"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T37"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T38"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T39"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T3P"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T41"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T48"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T49"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T4S"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T5O"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T5S"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("T66"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("T6A"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TA3"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TA4"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TAF"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TAL"));
+    assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("TAV"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("TBG"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TBM"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TC1"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TCP"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TCQ"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TCR"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TCY"));
+    assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("TDD"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TDY"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFE"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TFO"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("TFQ"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFT"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TGP"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TH6"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THC"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("THO"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THR"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("THX"));
+    assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("THZ"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TIH"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TLB"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TLC"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TLN"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMB"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMD"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TNB"));
+    assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("TNR"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TOX"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TP1"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TPC"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TPG"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TPH"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TPL"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TPO"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TPQ"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQI"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQQ"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRF"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("TRG"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRN"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRO"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRP"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRQ"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRW"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRX"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TS "));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TST"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TT "));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTD"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TTI"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTM"));
+    assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TTQ"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TTS"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY1"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY2"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY3"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY5"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYB"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYI"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYJ"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYN"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYO"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYQ"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYR"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYS"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYT"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TYU"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYW"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TYX"));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYY"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZB"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZO"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U  "));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U25"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2L"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2N"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2P"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U31"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U33"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U34"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U36"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U37"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U8U"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UAR"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UCL"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UD5"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UDP"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UFP"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFR"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFT"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("UMA"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMP"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN1"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN2"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UNK"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UR3"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("URD"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US1"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US2"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("US3"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US5"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("USM"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAD"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAF"));
+    assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAL"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("VB1"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VDL"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLL"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLM"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VMS"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VOL"));
+    assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("WCR"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("X  "));
+    assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("X2W"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("X4A"));
+    assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("X9Q"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAD"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAE"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAL"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAR"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCN"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("XCP"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCR"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XCS"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCT"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCY"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XGA"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGL"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGR"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGU"));
+    assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("XPR"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XSN"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTH"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTL"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTR"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XTS"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XTY"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XUA"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XUG"));
+    assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("XX1"));
+    assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("XXY"));
+    assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("XYG"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Y  "));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("YCM"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YG "));
+    assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("YOF"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("YRR"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YYG"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("Z  "));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Z01"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAD"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZBC"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZBU"));
+    assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("ZCL"));
+    assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZCY"));
+    assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZDU"));
+    assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ZFB"));
+    assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("ZGU"));
+    assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ZHP"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZTH"));
+    assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZU0"));
+    assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZZJ"));
+
     assertEquals(null, ResidueProperties.getCanonicalAminoAcid(null));
   }