test/jalview/schemes/ResiduePropertiesTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.schemes;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertNull;
  25
  26 import java.util.Collections;
  27 import java.util.List;
  28 import java.util.Map;
  29
  30 import org.testng.annotations.BeforeClass;
  31 import org.testng.annotations.Test;
  32
  33 import jalview.gui.JvOptionPane;
  34
  35 public class ResiduePropertiesTest
  36 {
  37
  38   @BeforeClass(alwaysRun = true)
  39   public void setUpJvOptionPane()
  40   {
  41     JvOptionPane.setInteractiveMode(false);
  42     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  43   }
  44
  45   /**
  46    * Test 'standard' codon translations (no ambiguity codes)
  47    */
  48   @Test(groups = { "Functional" })
  49   public void testCodonTranslate()
  50   {
  51     // standard translation table order column 1/2/3/4
  52     assertEquals("F", ResidueProperties.codonTranslate("TTT"));
  53     assertEquals("F", ResidueProperties.codonTranslate("TTC"));
  54     assertEquals("L", ResidueProperties.codonTranslate("TTA"));
  55     assertEquals("L", ResidueProperties.codonTranslate("TTG"));
  56     assertEquals("L", ResidueProperties.codonTranslate("CTT"));
  57     assertEquals("L", ResidueProperties.codonTranslate("CTC"));
  58     assertEquals("L", ResidueProperties.codonTranslate("CTA"));
  59     assertEquals("L", ResidueProperties.codonTranslate("CTG"));
  60     assertEquals("I", ResidueProperties.codonTranslate("ATT"));
  61     assertEquals("I", ResidueProperties.codonTranslate("ATC"));
  62     assertEquals("I", ResidueProperties.codonTranslate("ATA"));
  63     assertEquals("M", ResidueProperties.codonTranslate("ATG"));
  64     assertEquals("V", ResidueProperties.codonTranslate("GTT"));
  65     assertEquals("V", ResidueProperties.codonTranslate("GTC"));
  66     assertEquals("V", ResidueProperties.codonTranslate("GTA"));
  67     assertEquals("V", ResidueProperties.codonTranslate("GTG"));
  68     assertEquals("S", ResidueProperties.codonTranslate("TCT"));
  69     assertEquals("S", ResidueProperties.codonTranslate("TCC"));
  70     assertEquals("S", ResidueProperties.codonTranslate("TCA"));
  71     assertEquals("S", ResidueProperties.codonTranslate("TCG"));
  72     assertEquals("P", ResidueProperties.codonTranslate("CCT"));
  73     assertEquals("P", ResidueProperties.codonTranslate("CCC"));
  74     assertEquals("P", ResidueProperties.codonTranslate("CCA"));
  75     assertEquals("P", ResidueProperties.codonTranslate("CCG"));
  76     assertEquals("T", ResidueProperties.codonTranslate("ACT"));
  77     assertEquals("T", ResidueProperties.codonTranslate("ACC"));
  78     assertEquals("T", ResidueProperties.codonTranslate("ACA"));
  79     assertEquals("T", ResidueProperties.codonTranslate("ACG"));
  80     assertEquals("A", ResidueProperties.codonTranslate("GCT"));
  81     assertEquals("A", ResidueProperties.codonTranslate("GCC"));
  82     assertEquals("A", ResidueProperties.codonTranslate("GCA"));
  83     assertEquals("A", ResidueProperties.codonTranslate("GCG"));
  84     assertEquals("Y", ResidueProperties.codonTranslate("TAT"));
  85     assertEquals("Y", ResidueProperties.codonTranslate("TAC"));
  86     assertEquals("STOP", ResidueProperties.codonTranslate("TAA"));
  87     assertEquals("STOP", ResidueProperties.codonTranslate("TAG"));
  88     assertEquals("H", ResidueProperties.codonTranslate("CAT"));
  89     assertEquals("H", ResidueProperties.codonTranslate("CAC"));
  90     assertEquals("Q", ResidueProperties.codonTranslate("CAA"));
  91     assertEquals("Q", ResidueProperties.codonTranslate("CAG"));
  92     assertEquals("N", ResidueProperties.codonTranslate("AAT"));
  93     assertEquals("N", ResidueProperties.codonTranslate("AAC"));
  94     assertEquals("K", ResidueProperties.codonTranslate("AAA"));
  95     assertEquals("K", ResidueProperties.codonTranslate("AAG"));
  96     assertEquals("D", ResidueProperties.codonTranslate("GAT"));
  97     assertEquals("D", ResidueProperties.codonTranslate("GAC"));
  98     assertEquals("E", ResidueProperties.codonTranslate("GAA"));
  99     assertEquals("E", ResidueProperties.codonTranslate("GAG"));
 100     assertEquals("C", ResidueProperties.codonTranslate("TGT"));
 101     assertEquals("C", ResidueProperties.codonTranslate("TGC"));
 102     assertEquals("STOP", ResidueProperties.codonTranslate("TGA"));
 103     assertEquals("W", ResidueProperties.codonTranslate("TGG"));
 104     assertEquals("R", ResidueProperties.codonTranslate("CGT"));
 105     assertEquals("R", ResidueProperties.codonTranslate("CGC"));
 106     assertEquals("R", ResidueProperties.codonTranslate("CGA"));
 107     assertEquals("R", ResidueProperties.codonTranslate("CGG"));
 108     assertEquals("S", ResidueProperties.codonTranslate("AGT"));
 109     assertEquals("S", ResidueProperties.codonTranslate("AGC"));
 110     assertEquals("R", ResidueProperties.codonTranslate("AGA"));
 111     assertEquals("R", ResidueProperties.codonTranslate("AGG"));
 112     assertEquals("G", ResidueProperties.codonTranslate("GGT"));
 113     assertEquals("G", ResidueProperties.codonTranslate("GGC"));
 114     assertEquals("G", ResidueProperties.codonTranslate("GGA"));
 115     assertEquals("G", ResidueProperties.codonTranslate("GGG"));
 116   }
 117
 118   /**
 119    * Test a sample of codon translations involving ambiguity codes. Should
 120    * return a protein value where the ambiguity does not affect the translation.
 121    */
 122   @Test(groups = { "Functional" })
 123   public void testCodonTranslate_ambiguityCodes()
 124   {
 125     // Y is C or T
 126     assertEquals("C", ResidueProperties.codonTranslate("TGY"));
 127     // Phenylalanine first base variation
 128     assertEquals("L", ResidueProperties.codonTranslate("YTA"));
 129
 130     // W is A or T
 131     assertEquals("L", ResidueProperties.codonTranslate("CTW"));
 132     assertNull(ResidueProperties.codonTranslate("TTW"));
 133
 134     // S is G or C
 135     assertEquals("G", ResidueProperties.codonTranslate("GGS"));
 136     assertNull(ResidueProperties.codonTranslate("ATS"));
 137
 138     // K is T or G
 139     assertEquals("S", ResidueProperties.codonTranslate("TCK"));
 140     assertNull(ResidueProperties.codonTranslate("ATK"));
 141
 142     // M is C or A
 143     assertEquals("T", ResidueProperties.codonTranslate("ACM"));
 144     // Arginine first base variation
 145     assertEquals("R", ResidueProperties.codonTranslate("MGA"));
 146     assertEquals("R", ResidueProperties.codonTranslate("MGG"));
 147     assertNull(ResidueProperties.codonTranslate("TAM"));
 148
 149     // D is A, G or T
 150     assertEquals("P", ResidueProperties.codonTranslate("CCD"));
 151     assertNull(ResidueProperties.codonTranslate("AAD"));
 152
 153     // V is A, C or G
 154     assertEquals("V", ResidueProperties.codonTranslate("GTV"));
 155     assertNull(ResidueProperties.codonTranslate("TTV"));
 156
 157     // H is A, C or T
 158     assertEquals("A", ResidueProperties.codonTranslate("GCH"));
 159     assertEquals("I", ResidueProperties.codonTranslate("ATH"));
 160     assertNull(ResidueProperties.codonTranslate("AGH"));
 161
 162     // B is C, G or T
 163     assertEquals("P", ResidueProperties.codonTranslate("CCB"));
 164     assertNull(ResidueProperties.codonTranslate("TAB"));
 165
 166     // R is A or G
 167     // additional tests for JAL-1685 (resolved)
 168     assertEquals("L", ResidueProperties.codonTranslate("CTR"));
 169     assertEquals("V", ResidueProperties.codonTranslate("GTR"));
 170     assertEquals("S", ResidueProperties.codonTranslate("TCR"));
 171     assertEquals("P", ResidueProperties.codonTranslate("CCR"));
 172     assertEquals("T", ResidueProperties.codonTranslate("ACR"));
 173     assertEquals("A", ResidueProperties.codonTranslate("GCR"));
 174     assertEquals("R", ResidueProperties.codonTranslate("CGR"));
 175     assertEquals("G", ResidueProperties.codonTranslate("GGR"));
 176     assertEquals("R", ResidueProperties.codonTranslate("AGR"));
 177     assertEquals("E", ResidueProperties.codonTranslate("GAR"));
 178     assertEquals("K", ResidueProperties.codonTranslate("AAR"));
 179     assertEquals("L", ResidueProperties.codonTranslate("TTR"));
 180     assertEquals("Q", ResidueProperties.codonTranslate("CAR"));
 181     assertEquals("STOP", ResidueProperties.codonTranslate("TAR"));
 182     assertEquals("STOP", ResidueProperties.codonTranslate("TRA"));
 183     // Arginine first and third base ambiguity
 184     assertEquals("R", ResidueProperties.codonTranslate("MGR"));
 185     assertNull(ResidueProperties.codonTranslate("ATR"));
 186
 187     // N is any base; 8 proteins accept any base in 3rd position
 188     assertEquals("L", ResidueProperties.codonTranslate("CTN"));
 189     assertEquals("V", ResidueProperties.codonTranslate("GTN"));
 190     assertEquals("S", ResidueProperties.codonTranslate("TCN"));
 191     assertEquals("P", ResidueProperties.codonTranslate("CCN"));
 192     assertEquals("T", ResidueProperties.codonTranslate("ACN"));
 193     assertEquals("A", ResidueProperties.codonTranslate("GCN"));
 194     assertEquals("R", ResidueProperties.codonTranslate("CGN"));
 195     assertEquals("G", ResidueProperties.codonTranslate("GGN"));
 196     assertNull(ResidueProperties.codonTranslate("ATN"));
 197     assertNull(ResidueProperties.codonTranslate("ANT"));
 198     assertNull(ResidueProperties.codonTranslate("NAT"));
 199     assertNull(ResidueProperties.codonTranslate("ANN"));
 200     assertNull(ResidueProperties.codonTranslate("NNA"));
 201     assertNull(ResidueProperties.codonTranslate("NNN"));
 202
 203     // some random stuff
 204     assertNull(ResidueProperties.codonTranslate("YWB"));
 205     assertNull(ResidueProperties.codonTranslate("VHD"));
 206     assertNull(ResidueProperties.codonTranslate("WSK"));
 207   }
 208
 209   @Test(groups = { "Functional" })
 210   public void testGetResidues_nucleotide()
 211   {
 212     /*
 213      * Non-ambiguous only; we don't care about the order of the list, it is just
 214      * sorted here to make assertions reliable
 215      */
 216     List<String> residues = ResidueProperties.getResidues(true, false);
 217     Collections.sort(residues);
 218     assertEquals("[A, C, G, T, U]", residues.toString());
 219
 220     /*
 221      * Including ambiguity codes I N R X Y
 222      */
 223     residues = ResidueProperties.getResidues(true, true);
 224     Collections.sort(residues);
 225     assertEquals("[A, B, C, D, G, H, I, K, M, N, R, S, T, U, V, W, X, Y]",
 226             residues.toString());
 227   }
 228
 229   @Test(groups = { "Functional" })
 230   public void testGetResidues_peptide()
 231   {
 232     /*
 233      * Non-ambiguous only; we don't care about the order of the list, it is just
 234      * sorted here to make assertions reliable
 235      */
 236     List<String> residues = ResidueProperties.getResidues(false, false);
 237     Collections.sort(residues);
 238     assertEquals(
 239             "[ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL]",
 240             residues.toString());
 241
 242     /*
 243      * Including ambiguity codes ASX, GLX, XAA
 244      */
 245     residues = ResidueProperties.getResidues(false, true);
 246     Collections.sort(residues);
 247     assertEquals(
 248             "[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]",
 249             residues.toString());
 250   }
 251
 252   @Test(groups = { "Functional" })
 253   public void testGetCanonicalAminoAcid()
 254   {
 255     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
 256     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
 257
 258     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("00C"));
 259     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("01W"));
 260     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("02K"));
 261     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("03Y"));
 262     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("07O"));
 263     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("08P"));
 264     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0A0"));
 265     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("0A1"));
 266     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("0A2"));
 267     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0A8"));
 268     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AA"));
 269     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AB"));
 270     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AC"));
 271     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AD"));
 272     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("0AF"));
 273     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("0AG"));
 274     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("0AH"));
 275     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0AK"));
 276     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AM"));
 277     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0AP"));
 278     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0AU"));
 279     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AV"));
 280     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("0AZ"));
 281     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("0BN"));
 282     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0C "));
 283     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0CS"));
 284     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0DC"));
 285     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0DG"));
 286     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("0DT"));
 287     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0FL"));
 288     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0G "));
 289     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0NC"));
 290     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0SP"));
 291     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0U "));
 292     assertEquals("YG", ResidueProperties.getCanonicalAminoAcid("0YG"));
 293     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("10C"));
 294     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("125"));
 295     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("126"));
 296     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("127"));
 297     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("128"));
 298     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("12A"));
 299     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("143"));
 300     assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("175"));
 301     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("193"));
 302     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1AP"));
 303     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1MA"));
 304     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("1MG"));
 305     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("1PA"));
 306     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1PI"));
 307     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("1PR"));
 308     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("1SC"));
 309     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("1TQ"));
 310     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("1TY"));
 311     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("1X6"));
 312     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("200"));
 313     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("23F"));
 314     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("23S"));
 315     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("26B"));
 316     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AD"));
 317     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AG"));
 318     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AO"));
 319     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AR"));
 320     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AS"));
 321     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2AT"));
 322     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2AU"));
 323     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("2BD"));
 324     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2BT"));
 325     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2BU"));
 326     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2CO"));
 327     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2DA"));
 328     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DF"));
 329     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DM"));
 330     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2DO"));
 331     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2DT"));
 332     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2EG"));
 333     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FE"));
 334     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FI"));
 335     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("2FM"));
 336     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2GT"));
 337     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("2HF"));
 338     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2LU"));
 339     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2MA"));
 340     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2MG"));
 341     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2ML"));
 342     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("2MR"));
 343     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("2MT"));
 344     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2MU"));
 345     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2NT"));
 346     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2OM"));
 347     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2OT"));
 348     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2PI"));
 349     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2PR"));
 350     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2SA"));
 351     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2SI"));
 352     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2ST"));
 353     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2TL"));
 354     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("2TY"));
 355     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("2VA"));
 356     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2XA"));
 357     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32S"));
 358     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32T"));
 359     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("3AH"));
 360     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3AR"));
 361     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("3CF"));
 362     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3DA"));
 363     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("3DR"));
 364     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3GA"));
 365     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("3MD"));
 366     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("3ME"));
 367     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("3NF"));
 368     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("3QN"));
 369     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3TY"));
 370     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("3XH"));
 371     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4AC"));
 372     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("4BF"));
 373     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4CF"));
 374     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("4CY"));
 375     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4DP"));
 376     assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("4F3"));
 377     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("4FB"));
 378     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4FW"));
 379     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4HT"));
 380     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4IN"));
 381     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4MF"));
 382     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("4MM"));
 383     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4OC"));
 384     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PC"));
 385     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PD"));
 386     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PE"));
 387     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4PH"));
 388     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4SC"));
 389     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("4SU"));
 390     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4TA"));
 391     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("4U7"));
 392     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("56A"));
 393     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AA"));
 394     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AB"));
 395     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5AT"));
 396     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5BU"));
 397     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("5CG"));
 398     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CM"));
 399     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CS"));
 400     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5FA"));
 401     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5FC"));
 402     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5FU"));
 403     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("5HP"));
 404     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5HT"));
 405     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5HU"));
 406     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5IC"));
 407     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5IT"));
 408     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5IU"));
 409     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5MC"));
 410     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("5MD"));
 411     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5MU"));
 412     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5NC"));
 413     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5PC"));
 414     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5PY"));
 415     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5SE"));
 416     assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("5ZA"));
 417     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("64T"));
 418     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6CL"));
 419     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6CT"));
 420     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("6CW"));
 421     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6HA"));
 422     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("6HC"));
 423     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6HG"));
 424     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6HN"));
 425     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6HT"));
 426     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6IA"));
 427     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MA"));
 428     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MC"));
 429     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MI"));
 430     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MT"));
 431     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MZ"));
 432     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6OG"));
 433     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("70U"));
 434     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("7DA"));
 435     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7GU"));
 436     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("7JA"));
 437     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7MG"));
 438     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("8AN"));
 439     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8FG"));
 440     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8MG"));
 441     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8OG"));
 442     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("9NE"));
 443     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("9NF"));
 444     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("9NR"));
 445     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("9NV"));
 446     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A  "));
 447     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A1P"));
 448     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A23"));
 449     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2L"));
 450     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2M"));
 451     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A34"));
 452     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A35"));
 453     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A38"));
 454     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A39"));
 455     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3A"));
 456     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3P"));
 457     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A40"));
 458     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A43"));
 459     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A44"));
 460     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A47"));
 461     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5L"));
 462     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("A5M"));
 463     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A5N"));
 464     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5O"));
 465     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("A66"));
 466     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA3"));
 467     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA4"));
 468     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AAR"));
 469     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AB7"));
 470     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABA"));
 471     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABR"));
 472     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABS"));
 473     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ABT"));
 474     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ACB"));
 475     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ACL"));
 476     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AD2"));
 477     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ADD"));
 478     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ADX"));
 479     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AEA"));
 480     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AEI"));
 481     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AET"));
 482     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFA"));
 483     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFF"));
 484     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("AFG"));
 485     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AGM"));
 486     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("AGT"));
 487     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AHB"));
 488     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHH"));
 489     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHO"));
 490     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHP"));
 491     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHS"));
 492     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHT"));
 493     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AIB"));
 494     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKL"));
 495     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKZ"));
 496     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALA"));
 497     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALC"));
 498     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALM"));
 499     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALN"));
 500     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ALO"));
 501     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ALQ"));
 502     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALS"));
 503     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALT"));
 504     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALV"));
 505     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ALY"));
 506     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AN8"));
 507     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AP7"));
 508     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APE"));
 509     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("APH"));
 510     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("API"));
 511     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("APK"));
 512     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APM"));
 513     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APP"));
 514     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR2"));
 515     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("AR4"));
 516     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR7"));
 517     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARG"));
 518     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARM"));
 519     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARO"));
 520     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ARV"));
 521     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AS "));
 522     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AS2"));
 523     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AS9"));
 524     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASA"));
 525     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASB"));
 526     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASI"));
 527     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASK"));
 528     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASL"));
 529     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ASM"));
 530     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASN"));
 531     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASP"));
 532     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASQ"));
 533     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASU"));
 534     assertEquals("ASX", ResidueProperties.getCanonicalAminoAcid("ASX"));
 535     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATD"));
 536     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATL"));
 537     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATM"));
 538     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AVC"));
 539     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AVN"));
 540     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AYA"));
 541     assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("AYG"));
 542     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("AZK"));
 543     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("AZS"));
 544     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("AZY"));
 545     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B1F"));
 546     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B1P"));
 547     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B2A"));
 548     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B2F"));
 549     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("B2I"));
 550     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("B2V"));
 551     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B3A"));
 552     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("B3D"));
 553     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("B3E"));
 554     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("B3K"));
 555     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3L"));
 556     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3M"));
 557     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3Q"));
 558     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("B3S"));
 559     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3T"));
 560     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("B3U"));
 561     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B3X"));
 562     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("B3Y"));
 563     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB6"));
 564     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB7"));
 565     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BB8"));
 566     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB9"));
 567     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BBC"));
 568     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BCS"));
 569     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BE2"));
 570     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BFD"));
 571     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BG1"));
 572     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("BGM"));
 573     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BH2"));
 574     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BHD"));
 575     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BIF"));
 576     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BIL"));
 577     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("BIU"));
 578     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BJH"));
 579     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BLE"));
 580     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("BLY"));
 581     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BMP"));
 582     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BMT"));
 583     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BNN"));
 584     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BNO"));
 585     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BOE"));
 586     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("BOR"));
 587     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BPE"));
 588     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BRU"));
 589     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BSE"));
 590     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BT5"));
 591     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BTA"));
 592     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BTC"));
 593     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("BTR"));
 594     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BUC"));
 595     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("BUG"));
 596     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BVP"));
 597     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BZG"));
 598     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C  "));
 599     assertEquals("TYG", ResidueProperties.getCanonicalAminoAcid("C12"));
 600     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("C1X"));
 601     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C25"));
 602     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2L"));
 603     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2S"));
 604     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C31"));
 605     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C32"));
 606     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C34"));
 607     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C36"));
 608     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C37"));
 609     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C38"));
 610     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C3Y"));
 611     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C42"));
 612     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C43"));
 613     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C45"));
 614     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C46"));
 615     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C49"));
 616     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4R"));
 617     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4S"));
 618     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C5C"));
 619     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("C66"));
 620     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C6C"));
 621     assertEquals("TFG", ResidueProperties.getCanonicalAminoAcid("C99"));
 622     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAF"));
 623     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAL"));
 624     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAR"));
 625     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAS"));
 626     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAV"));
 627     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAY"));
 628     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CB2"));
 629     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBR"));
 630     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBV"));
 631     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCC"));
 632     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CCL"));
 633     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCS"));
 634     assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("CCY"));
 635     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDE"));
 636     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDV"));
 637     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CDW"));
 638     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CEA"));
 639     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CFL"));
 640     assertEquals("FCYG", ResidueProperties.getCanonicalAminoAcid("CFY")); // check
 641     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CG1"));
 642     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGA"));
 643     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGU"));
 644     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CH "));
 645     assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CH6"));
 646     assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CH7"));
 647     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHF"));
 648     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHG"));
 649     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CHP"));
 650     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHS"));
 651     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("CIR"));
 652     assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CJO"));
 653     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("CLE"));
 654     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLG"));
 655     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLH"));
 656     assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("CLV"));
 657     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CM0"));
 658     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CME"));
 659     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMH"));
 660     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CML"));
 661     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMR"));
 662     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMT"));
 663     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("CNU"));
 664     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CP1"));
 665     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPC"));
 666     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPI"));
 667     assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CQR"));
 668     assertEquals("TLG", ResidueProperties.getCanonicalAminoAcid("CR0"));
 669     assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CR2"));
 670     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CR5"));
 671     assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CR7"));
 672     assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("CR8"));
 673     assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("CRF"));
 674     assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("CRG"));
 675     assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CRK"));
 676     assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CRO"));
 677     assertEquals("QYG", ResidueProperties.getCanonicalAminoAcid("CRQ"));
 678     assertEquals("EYG", ResidueProperties.getCanonicalAminoAcid("CRU"));
 679     assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRW"));
 680     assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRX"));
 681     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS0"));
 682     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS1"));
 683     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS3"));
 684     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS4"));
 685     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CS8"));
 686     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSA"));
 687     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSB"));
 688     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSD"));
 689     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSE"));
 690     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSF"));
 691     assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("CSH"));
 692     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CSI"));
 693     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSJ"));
 694     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSL"));
 695     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSO"));
 696     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSP"));
 697     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSR"));
 698     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSS"));
 699     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSU"));
 700     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSW"));
 701     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSX"));
 702     assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("CSY"));
 703     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSZ"));
 704     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("CTE"));
 705     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTG"));
 706     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTH"));
 707     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CUC"));
 708     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("CWR"));
 709     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("CXM"));
 710     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY0"));
 711     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY1"));
 712     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY3"));
 713     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY4"));
 714     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYA"));
 715     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYD"));
 716     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYF"));
 717     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYG"));
 718     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CYJ"));
 719     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYM"));
 720     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYQ"));
 721     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYR"));
 722     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYS"));
 723     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZ2"));
 724     assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CZO"));
 725     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZZ"));
 726     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D11"));
 727     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D1P"));
 728     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D3 "));
 729     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D33"));
 730     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("D3P"));
 731     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D3T"));
 732     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D4M"));
 733     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("D4P"));
 734     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DA "));
 735     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DA2"));
 736     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAB"));
 737     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DAH"));
 738     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAL"));
 739     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DAR"));
 740     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DAS"));
 741     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBB"));
 742     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DBM"));
 743     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DBS"));
 744     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBU"));
 745     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DBY"));
 746     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DBZ"));
 747     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC "));
 748     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC2"));
 749     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DCG"));
 750     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCI"));
 751     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCL"));
 752     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCT"));
 753     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCY"));
 754     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DDE"));
 755     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DDG"));
 756     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DDN"));
 757     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DDX"));
 758     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DFC"));
 759     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DFG"));
 760     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFI"));
 761     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFO"));
 762     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DFT"));
 763     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DG "));
 764     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGH"));
 765     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGI"));
 766     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("DGL"));
 767     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("DGN"));
 768     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DHA"));
 769     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DHI"));
 770     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHL"));
 771     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHN"));
 772     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHP"));
 773     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DHU"));
 774     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHV"));
 775     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DI "));
 776     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DIL"));
 777     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DIR"));
 778     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DIV"));
 779     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DLE"));
 780     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLS"));
 781     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLY"));
 782     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DM0"));
 783     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DMH"));
 784     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DMK"));
 785     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DMT"));
 786     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DN "));
 787     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNE"));
 788     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNG"));
 789     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNL"));
 790     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNM"));
 791     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DNP"));
 792     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DNR"));
 793     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNS"));
 794     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DOA"));
 795     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DOC"));
 796     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DOH"));
 797     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DON"));
 798     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DPB"));
 799     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DPH"));
 800     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPL"));
 801     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DPP"));
 802     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DPQ"));
 803     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPR"));
 804     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DPY"));
 805     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DRM"));
 806     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRP"));
 807     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DRT"));
 808     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRZ"));
 809     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSE"));
 810     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DSG"));
 811     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSN"));
 812     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DSP"));
 813     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DT "));
 814     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DTH"));
 815     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("DTR"));
 816     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DTY"));
 817     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DU "));
 818     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DVA"));
 819     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXD"));
 820     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXN"));
 821     assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("DYG"));
 822     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DYS"));
 823     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DZM"));
 824     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E  "));
 825     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E1X"));
 826     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("ECC"));
 827     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("EDA"));
 828     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("EFC"));
 829     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("EHP"));
 830     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("EIT"));
 831     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ENP"));
 832     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("ESB"));
 833     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("ESC"));
 834     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EXB"));
 835     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("EXY"));
 836     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("EY5"));
 837     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EYS"));
 838     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("F2F"));
 839     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FA2"));
 840     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FA5"));
 841     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAG"));
 842     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAI"));
 843     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB5"));
 844     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB6"));
 845     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FCL"));
 846     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FFD"));
 847     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("FGA"));
 848     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FGL"));
 849     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("FGP"));
 850     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FHL"));
 851     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FHO"));
 852     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("FHU"));
 853     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FLA"));
 854     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("FLE"));
 855     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FLT"));
 856     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("FME"));
 857     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FMG"));
 858     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FMU"));
 859     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("FOE"));
 860     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FOX"));
 861     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("FP9"));
 862     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FPA"));
 863     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FRD"));
 864     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FT6"));
 865     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FTR"));
 866     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FTY"));
 867     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("FVA"));
 868     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FZN"));
 869     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G  "));
 870     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G25"));
 871     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2L"));
 872     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2S"));
 873     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G31"));
 874     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G32"));
 875     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G33"));
 876     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G36"));
 877     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G38"));
 878     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G42"));
 879     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G46"));
 880     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G47"));
 881     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G48"));
 882     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G49"));
 883     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("G4P"));
 884     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G7M"));
 885     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GAO"));
 886     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GAU"));
 887     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GCK"));
 888     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GCM"));
 889     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDP"));
 890     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDR"));
 891     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GFL"));
 892     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GGL"));
 893     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GH3"));
 894     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GHG"));
 895     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GHP"));
 896     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GL3"));
 897     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLH"));
 898     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLJ"));
 899     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLK"));
 900     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GLM"));
 901     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLN"));
 902     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLQ"));
 903     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLU"));
 904     assertEquals("GLX", ResidueProperties.getCanonicalAminoAcid("GLX"));
 905     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLY"));
 906     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLZ"));
 907     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GMA"));
 908     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GMS"));
 909     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("GMU"));
 910     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GN7"));
 911     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GND"));
 912     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("GNE"));
 913     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GOM"));
 914     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("GPL"));
 915     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GS "));
 916     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSC"));
 917     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSR"));
 918     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSS"));
 919     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GSU"));
 920     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GT9"));
 921     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GTP"));
 922     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GVL"));
 923     assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("GYC"));
 924     assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("GYS"));
 925     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("H2U"));
 926     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("H5M"));
 927     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HAC"));
 928     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HAR"));
 929     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HBN"));
 930     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HCS"));
 931     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HDP"));
 932     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HEU"));
 933     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HFA"));
 934     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HGL"));
 935     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HHI"));
 936     assertEquals("AK", ResidueProperties.getCanonicalAminoAcid("HHK")); // check
 937     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIA"));
 938     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIC"));
 939     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIP"));
 940     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIQ"));
 941     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIS"));
 942     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HL2"));
 943     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HLU"));
 944     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HMR"));
 945     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HOL"));
 946     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPC"));
 947     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPE"));
 948     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPH"));
 949     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPQ"));
 950     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HQA"));
 951     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HRG"));
 952     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HRP"));
 953     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS8"));
 954     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS9"));
 955     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSE"));
 956     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSL"));
 957     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HSO"));
 958     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("HTI"));
 959     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HTN"));
 960     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HTR"));
 961     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HV5"));
 962     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("HVA"));
 963     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HY3"));
 964     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HYP"));
 965     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HZP"));
 966     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I  "));
 967     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I2M"));
 968     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("I58"));
 969     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("I5C"));
 970     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("IAM"));
 971     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("IAR"));
 972     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("IAS"));
 973     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IC "));
 974     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IEL"));
 975     assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("IEY"));
 976     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IG "));
 977     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGL"));
 978     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGU"));
 979     assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("IIC"));
 980     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IIL"));
 981     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILE"));
 982     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("ILG"));
 983     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILX"));
 984     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IMC"));
 985     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IML"));
 986     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("IOY"));
 987     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IPG"));
 988     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IPN"));
 989     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IRN"));
 990     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IT1"));
 991     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("IU "));
 992     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("IYR"));
 993     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("IYT"));
 994     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("IZO"));
 995     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJJ"));
 996     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJK"));
 997     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJL"));
 998     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("JW5"));
 999     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("K1R"));
1000     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("KAG"));
1001     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KCX"));
1002     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KGC"));
1003     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("KNB"));
1004     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("KOR"));
1005     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KPI"));
1006     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KST"));
1007     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KYQ"));
1008     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("L2A"));
1009     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LA2"));
1010     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("LAA"));
1011     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LAL"));
1012     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LBY"));
1013     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("LC "));
1014     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LCA"));
1015     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCC"));
1016     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LCG"));
1017     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCH"));
1018     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCK"));
1019     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCX"));
1020     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LDH"));
1021     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LED"));
1022     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEF"));
1023     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEH"));
1024     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LEI"));
1025     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEM"));
1026     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEN"));
1027     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LET"));
1028     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEU"));
1029     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEX"));
1030     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LG "));
1031     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LGP"));
1032     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LHC"));
1033     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("LHU"));
1034     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LKC"));
1035     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLP"));
1036     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLY"));
1037     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("LME"));
1038     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LMF"));
1039     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("LMQ"));
1040     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LMS"));
1041     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LP6"));
1042     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("LPD"));
1043     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LPG"));
1044     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LPL"));
1045     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("LPS"));
1046     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LSO"));
1047     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LTA"));
1048     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("LTR"));
1049     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LVG"));
1050     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LVN"));
1051     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYF"));
1052     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYK"));
1053     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYM"));
1054     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYN"));
1055     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYR"));
1056     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYS"));
1057     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYX"));
1058     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYZ"));
1059     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M0H"));
1060     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M1G"));
1061     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M2G"));
1062     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M2L"));
1063     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("M2S"));
1064     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M30"));
1065     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M3L"));
1066     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M5M"));
1067     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA "));
1068     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA6"));
1069     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA7"));
1070     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAA"));
1071     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAD"));
1072     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MAI"));
1073     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MBQ"));
1074     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MBZ"));
1075     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MC1"));
1076     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MCG"));
1077     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MCL"));
1078     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCS"));
1079     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCY"));
1080     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MD3"));
1081     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MD6"));
1082     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MDH"));
1083     assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("MDO"));
1084     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MDR"));
1085     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("MEA"));
1086     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MED"));
1087     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("MEG"));
1088     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MEN"));
1089     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MEP"));
1090     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MEQ"));
1091     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
1092     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MEU"));
1093     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MF3"));
1094     assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("MFC"));
1095     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MG1"));
1096     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MGG"));
1097     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MGN"));
1098     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MGQ"));
1099     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGV"));
1100     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGY"));
1101     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MHL"));
1102     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MHO"));
1103     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("MHS"));
1104     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MIA"));
1105     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MIS"));
1106     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MK8"));
1107     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ML3"));
1108     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLE"));
1109     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLL"));
1110     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLY"));
1111     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLZ"));
1112     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MME"));
1113     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MMO"));
1114     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MMT"));
1115     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MND"));
1116     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MNL"));
1117     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MNU"));
1118     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MNV"));
1119     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MOD"));
1120     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("MP8"));
1121     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPH"));
1122     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPJ"));
1123     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MPQ"));
1124     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MRG"));
1125     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MSA"));
1126     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
1127     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSL"));
1128     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSO"));
1129     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MSP"));
1130     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MT2"));
1131     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MTR"));
1132     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MTU"));
1133     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MTY"));
1134     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MVA"));
1135     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N  "));
1136     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("N10"));
1137     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("N2C"));
1138     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N5I"));
1139     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("N5M"));
1140     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("N6G"));
1141     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("N7P"));
1142     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NA8"));
1143     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAL"));
1144     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAM"));
1145     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NB8"));
1146     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NBQ"));
1147     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("NC1"));
1148     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NCB"));
1149     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NCX"));
1150     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NCY"));
1151     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NDF"));
1152     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("NDN"));
1153     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEM"));
1154     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEP"));
1155     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NF2"));
1156     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NFA"));
1157     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("NHL"));
1158     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NIT"));
1159     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NIY"));
1160     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLE"));
1161     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLN"));
1162     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLO"));
1163     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLP"));
1164     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("NLQ"));
1165     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("NMC"));
1166     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NMM"));
1167     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMS"));
1168     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMT"));
1169     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NNH"));
1170     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NP3"));
1171     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NPH"));
1172     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NPI"));
1173     assertEquals("LYG", ResidueProperties.getCanonicalAminoAcid("NRP"));
1174     assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("NRQ"));
1175     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NSK"));
1176     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NTY"));
1177     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("NVA"));
1178     assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("NYC"));
1179     assertEquals("NYG", ResidueProperties.getCanonicalAminoAcid("NYG"));
1180     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NYM"));
1181     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NYS"));
1182     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NZH"));
1183     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("O12"));
1184     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("O2C"));
1185     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("O2G"));
1186     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("OAD"));
1187     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OAS"));
1188     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBF"));
1189     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBS"));
1190     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCS"));
1191     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCY"));
1192     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ODP"));
1193     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("OHI"));
1194     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OHS"));
1195     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OIC"));
1196     assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("OIP"));
1197     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OLE"));
1198     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OLT"));
1199     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OLZ"));
1200     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OMC"));
1201     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("OMG"));
1202     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("OMT"));
1203     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("OMU"));
1204     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ONE"));
1205     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ONH"));
1206     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ONL"));
1207     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("OPR"));
1208     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ORN"));
1209     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ORQ"));
1210     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OSE"));
1211     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OTB"));
1212     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OTH"));
1213     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("OTY"));
1214     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OXX"));
1215     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("P  "));
1216     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("P1L"));
1217     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("P1P"));
1218     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("P2T"));
1219     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("P2U"));
1220     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("P2Y"));
1221     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("P5P"));
1222     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PAQ"));
1223     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PAS"));
1224     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("PAT"));
1225     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PAU"));
1226     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PBB"));
1227     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PBF"));
1228     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PBT"));
1229     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("PCA"));
1230     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PCC"));
1231     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PCE"));
1232     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PCS"));
1233     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PDL"));
1234     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PDU"));
1235     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PEC"));
1236     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PF5"));
1237     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PFF"));
1238     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PFX"));
1239     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("PG1"));
1240     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG7"));
1241     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG9"));
1242     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PGL"));
1243     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGN"));
1244     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGP"));
1245     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGY"));
1246     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHA"));
1247     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PHD"));
1248     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHE"));
1249     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHI"));
1250     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHL"));
1251     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHM"));
1252     assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("PIA"));
1253     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PIV"));
1254     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("PLE"));
1255     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PM3"));
1256     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PMT"));
1257     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("POM"));
1258     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PPN"));
1259     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PPU"));
1260     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PPW"));
1261     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PQ1"));
1262     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PR3"));
1263     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PR5"));
1264     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PR9"));
1265     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PRN"));
1266     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRO"));
1267     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRS"));
1268     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PSA"));
1269     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PSH"));
1270     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("PST"));
1271     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PSU"));
1272     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PSW"));
1273     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PTA"));
1274     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTH"));
1275     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTM"));
1276     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTR"));
1277     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PU "));
1278     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PUY"));
1279     assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PVH"));
1280     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PVL"));
1281     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PYA"));
1282     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PYO"));
1283     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PYX"));
1284     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PYY"));
1285     assertEquals("QLG", ResidueProperties.getCanonicalAminoAcid("QLG"));
1286     assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("QMM"));
1287     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("QPA"));
1288     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("QPH"));
1289     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("QUO"));
1290     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("R  "));
1291     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("R1A"));
1292     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("R4K"));
1293     assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("RC7"));
1294     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE0"));
1295     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE3"));
1296     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RIA"));
1297     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RMP"));
1298     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("RON"));
1299     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("RT "));
1300     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("RTP"));
1301     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("S1H"));
1302     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S2C"));
1303     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2D"));
1304     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("S2M"));
1305     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2P"));
1306     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S4A"));
1307     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S4C"));
1308     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S4G"));
1309     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("S4U"));
1310     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S6G"));
1311     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SAC"));
1312     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SAH"));
1313     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SAR"));
1314     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SBL"));
1315     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SC "));
1316     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCH"));
1317     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCS"));
1318     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCY"));
1319     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SD2"));
1320     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SDG"));
1321     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SDP"));
1322     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEB"));
1323     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEC"));
1324     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEG"));
1325     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEL"));
1326     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEM"));
1327     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEN"));
1328     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEP"));
1329     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SER"));
1330     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SET"));
1331     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SGB"));
1332     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SHC"));
1333     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SHP"));
1334     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SHR"));
1335     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SIB"));
1336     assertEquals("DC", ResidueProperties.getCanonicalAminoAcid("SIC")); // check
1337     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLA"));
1338     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLR"));
1339     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SLZ"));
1340     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SMC"));
1341     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("SME"));
1342     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("SMF"));
1343     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SMP"));
1344     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SMT"));
1345     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SNC"));
1346     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SNN"));
1347     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SOC"));
1348     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SOS"));
1349     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SOY"));
1350     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SPT"));
1351     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SRA"));
1352     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SSU"));
1353     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("STY"));
1354     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SUB"));
1355     assertEquals("DG", ResidueProperties.getCanonicalAminoAcid("SUI"));
1356     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SUN"));
1357     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SUR"));
1358     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVA"));
1359     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVV"));
1360     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVW"));
1361     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVX"));
1362     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVY"));
1363     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SVZ"));
1364     assertEquals("SWG", ResidueProperties.getCanonicalAminoAcid("SWG"));
1365     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SYS"));
1366     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T  "));
1367     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("T11"));
1368     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T23"));
1369     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T2S"));
1370     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("T2T"));
1371     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T31"));
1372     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T32"));
1373     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T36"));
1374     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T37"));
1375     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T38"));
1376     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T39"));
1377     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T3P"));
1378     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T41"));
1379     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T48"));
1380     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T49"));
1381     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T4S"));
1382     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T5O"));
1383     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T5S"));
1384     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("T66"));
1385     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("T6A"));
1386     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TA3"));
1387     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TA4"));
1388     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TAF"));
1389     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TAL"));
1390     assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("TAV"));
1391     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("TBG"));
1392     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TBM"));
1393     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TC1"));
1394     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TCP"));
1395     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TCQ"));
1396     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TCR"));
1397     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TCY"));
1398     assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("TDD"));
1399     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TDY"));
1400     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFE"));
1401     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TFO"));
1402     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("TFQ"));
1403     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFT"));
1404     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TGP"));
1405     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TH6"));
1406     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THC"));
1407     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("THO"));
1408     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THR"));
1409     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("THX"));
1410     assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("THZ"));
1411     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TIH"));
1412     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TLB"));
1413     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TLC"));
1414     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TLN"));
1415     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMB"));
1416     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMD"));
1417     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TNB"));
1418     assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("TNR"));
1419     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TOX"));
1420     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TP1"));
1421     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TPC"));
1422     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TPG"));
1423     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TPH"));
1424     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TPL"));
1425     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TPO"));
1426     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TPQ"));
1427     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQI"));
1428     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQQ"));
1429     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRF"));
1430     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("TRG"));
1431     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRN"));
1432     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRO"));
1433     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRP"));
1434     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRQ"));
1435     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRW"));
1436     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRX"));
1437     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TS "));
1438     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TST"));
1439     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TT "));
1440     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTD"));
1441     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TTI"));
1442     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTM"));
1443     assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TTQ"));
1444     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TTS"));
1445     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY1"));
1446     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY2"));
1447     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY3"));
1448     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY5"));
1449     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYB"));
1450     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYI"));
1451     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYJ"));
1452     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYN"));
1453     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYO"));
1454     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYQ"));
1455     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYR"));
1456     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYS"));
1457     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYT"));
1458     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TYU"));
1459     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYW"));
1460     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TYX"));
1461     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYY"));
1462     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZB"));
1463     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZO"));
1464     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U  "));
1465     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U25"));
1466     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2L"));
1467     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2N"));
1468     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2P"));
1469     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U31"));
1470     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U33"));
1471     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U34"));
1472     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U36"));
1473     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U37"));
1474     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U8U"));
1475     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UAR"));
1476     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UCL"));
1477     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UD5"));
1478     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UDP"));
1479     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UFP"));
1480     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFR"));
1481     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFT"));
1482     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("UMA"));
1483     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMP"));
1484     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMS"));
1485     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN1"));
1486     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN2"));
1487     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UNK"));
1488     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UR3"));
1489     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("URD"));
1490     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US1"));
1491     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US2"));
1492     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("US3"));
1493     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US5"));
1494     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("USM"));
1495     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAD"));
1496     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAF"));
1497     assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAL"));
1498     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("VB1"));
1499     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VDL"));
1500     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLL"));
1501     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLM"));
1502     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VMS"));
1503     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VOL"));
1504     assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("WCR"));
1505     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("X  "));
1506     assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("X2W"));
1507     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("X4A"));
1508     assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("X9Q"));
1509     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAD"));
1510     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAE"));
1511     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAL"));
1512     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAR"));
1513     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCL"));
1514     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCN"));
1515     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("XCP"));
1516     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCR"));
1517     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XCS"));
1518     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCT"));
1519     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCY"));
1520     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XGA"));
1521     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGL"));
1522     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGR"));
1523     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGU"));
1524     assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("XPR"));
1525     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XSN"));
1526     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTH"));
1527     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTL"));
1528     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTR"));
1529     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XTS"));
1530     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XTY"));
1531     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XUA"));
1532     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XUG"));
1533     assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("XX1"));
1534     assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("XXY"));
1535     assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("XYG"));
1536     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Y  "));
1537     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("YCM"));
1538     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YG "));
1539     assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("YOF"));
1540     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("YRR"));
1541     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YYG"));
1542     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("Z  "));
1543     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Z01"));
1544     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAD"));
1545     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAL"));
1546     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZBC"));
1547     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZBU"));
1548     assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("ZCL"));
1549     assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZCY"));
1550     assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZDU"));
1551     assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ZFB"));
1552     assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("ZGU"));
1553     assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ZHP"));
1554     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZTH"));
1555     assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZU0"));
1556     assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZZJ"));
1557
1558     assertEquals(null, ResidueProperties.getCanonicalAminoAcid(null));
1559   }
1560
1561   @Test(groups = { "Functional" })
1562   public void testGetSingleCharacterCode()
1563   {
1564     assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
1565     assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
1566     assertEquals('0', ResidueProperties.getSingleCharacterCode(""));
1567     assertEquals('Q', ResidueProperties.getSingleCharacterCode("GLN"));
1568     assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln"));
1569     assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln"));
1570   }
1571
1572   @Test(groups = { "Functional" })
1573   public void testGetDssp3State()
1574   {
1575     assertNull(ResidueProperties.getDssp3state(null));
1576     assertEquals("", ResidueProperties.getDssp3state(""));
1577     String foo = "0123 []<>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ";
1578     String bar = "                                    E  E HHH                 ";
1579     assertEquals(bar, ResidueProperties.getDssp3state(foo));
1580   }
1581
1582   @Test(groups = { "Functional" })
1583   public void testPhysicoChemicalProperties()
1584   {
1585     checkProperty("aromatic", "FYWH-*");
1586     checkProperty("aliphatic", "IVL-*");
1587     checkProperty("tiny", "GAS-*");
1588     checkProperty("small", "VCTGACSDNP-*");
1589     checkProperty("charged", "HKRDE-*");
1590     checkProperty("negative", "DE-*");
1591     checkProperty("polar", "YWHRKTSNDEQ-*X");
1592     checkProperty("positive", "HKR-*");
1593     checkProperty("proline", "P-*");
1594     checkProperty("hydrophobic", "MILVFYWHKTGAC-*X");
1595   }
1596
1597   /**
1598    * Verify that the residues in the list have the named property, and other
1599    * residues do not
1600    *
1601    * @param property
1602    * @param residues
1603    */
1604   void checkProperty(String property, String residues)
1605   {
1606     Map<String, Integer> props = ResidueProperties.propHash.get(property);
1607
1608     /*
1609      * assert residues have the property (value 1 in lookup)
1610      */
1611     for (char res : residues.toCharArray())
1612     {
1613       assertEquals(res + " should be " + property, 1,
1614               props.get(String.valueOf(res)).intValue());
1615     }
1616
1617     /*
1618      * assert other residues do not (value 0 in lookup)
1619      */
1620     for (String res : ResidueProperties.aa)
1621     {
1622       if (!residues.contains(res))
1623       {
1624         Integer propValue = props.get(String.valueOf(res));
1625
1626         if (propValue != null)
1627         {
1628           /*
1629            * conservation calculation assigns unexpected symbols
1630            * the same value as '-'; here we just check those which
1631            * explicitly do not have the property
1632            */
1633           assertEquals(res + " should not be " + property, 0,
1634                   propValue.intValue());
1635         }
1636       }
1637     }
1638   }
1639 }