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